Starting phenix.real_space_refine on Tue Mar 3 23:11:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vku_32019/03_2026/7vku_32019_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vku_32019/03_2026/7vku_32019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vku_32019/03_2026/7vku_32019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vku_32019/03_2026/7vku_32019.map" model { file = "/net/cci-nas-00/data/ceres_data/7vku_32019/03_2026/7vku_32019_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vku_32019/03_2026/7vku_32019_neut.cif" } resolution = 3.2 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= 0.010 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 39 5.16 5 C 5902 2.51 5 N 1565 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 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: 9219 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3314 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 16, 'TRANS': 401} Chain breaks: 2 Chain: "B" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2460 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 2 Chain: "C" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2227 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 6, 'TRANS': 268} Chain breaks: 2 Chain: "X" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 6 Time building chain proxies: 2.11, per 1000 atoms: 0.23 Number of scatterers: 9219 At special positions: 0 Unit cell: (99.6, 95.865, 126.99, 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 39 16.00 O 1713 8.00 N 1565 7.00 C 5902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.66 Conformation dependent library (CDL) restraints added in 331.5 milliseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 32.6% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.730A pdb=" N ALA A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.647A pdb=" N ASP A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 434 Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.580A pdb=" N ASP B 16 " --> pdb=" O LYS B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 12 through 16' Processing helix chain 'B' and resid 32 through 40 removed outlier: 3.588A pdb=" N GLN B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 142 through 150 Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.666A pdb=" N MET B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 181 Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.632A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.587A pdb=" N GLU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.562A pdb=" N SER B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.624A pdb=" N GLN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.830A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 34 through 38 removed outlier: 4.000A pdb=" N LYS C 38 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 4.073A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 121 through 130 removed outlier: 4.015A pdb=" N LEU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.723A pdb=" N LYS C 147 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 148 " --> pdb=" O PHE C 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 148' Processing helix chain 'C' and resid 156 through 170 removed outlier: 3.548A pdb=" N GLU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 241 removed outlier: 3.611A pdb=" N LYS C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR C 221 " --> pdb=" O GLN C 217 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 263 removed outlier: 3.596A pdb=" N LEU C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 4.161A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.904A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 324 removed outlier: 4.376A pdb=" N ASN C 321 " --> pdb=" O MET C 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 removed outlier: 7.573A pdb=" N VAL A 35 " --> pdb=" O LEU A 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.595A pdb=" N SER A 192 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 180 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 185 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 241 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 416 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 443 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 480 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466 Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AA5, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.625A pdb=" N LEU C 65 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 210 through 214 removed outlier: 3.713A pdb=" N GLY X 212 " --> pdb=" O LEU X 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 244 through 245 Processing sheet with id=AA9, first strand: chain 'X' and resid 302 through 304 382 hydrogen bonds defined for protein. 1074 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: 1.57 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.34: 2951 1.34 - 1.52: 5452 1.52 - 1.71: 935 1.71 - 1.89: 57 1.89 - 2.07: 1 Bond restraints: 9396 Sorted by residual: bond pdb=" C ALA X 264 " pdb=" N ASN X 266 " ideal model delta sigma weight residual 1.332 2.067 -0.735 1.34e-02 5.57e+03 3.01e+03 bond pdb=" CA LEU C 100 " pdb=" C LEU C 100 " ideal model delta sigma weight residual 1.523 1.411 0.112 1.34e-02 5.57e+03 6.99e+01 bond pdb=" CA LYS C 38 " pdb=" C LYS C 38 " ideal model delta sigma weight residual 1.520 1.425 0.095 1.40e-02 5.10e+03 4.59e+01 bond pdb=" CA LEU X 183 " pdb=" C LEU X 183 " ideal model delta sigma weight residual 1.526 1.443 0.082 1.28e-02 6.10e+03 4.13e+01 bond pdb=" C LEU C 100 " pdb=" O LEU C 100 " ideal model delta sigma weight residual 1.235 1.163 0.073 1.26e-02 6.30e+03 3.32e+01 ... (remaining 9391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 12388 3.37 - 6.73: 254 6.73 - 10.10: 36 10.10 - 13.46: 8 13.46 - 16.83: 4 Bond angle restraints: 12690 Sorted by residual: angle pdb=" N LYS C 38 " pdb=" CA LYS C 38 " pdb=" C LYS C 38 " ideal model delta sigma weight residual 114.04 98.35 15.69 1.24e+00 6.50e-01 1.60e+02 angle pdb=" C ALA X 264 " pdb=" N ASN X 266 " pdb=" CA ASN X 266 " ideal model delta sigma weight residual 122.65 108.95 13.70 1.60e+00 3.91e-01 7.33e+01 angle pdb=" N GLY X 195 " pdb=" CA GLY X 195 " pdb=" C GLY X 195 " ideal model delta sigma weight residual 110.69 127.52 -16.83 2.05e+00 2.38e-01 6.74e+01 angle pdb=" O ALA X 264 " pdb=" C ALA X 264 " pdb=" N ASN X 266 " ideal model delta sigma weight residual 122.59 133.04 -10.45 1.33e+00 5.65e-01 6.17e+01 angle pdb=" N LEU X 183 " pdb=" CA LEU X 183 " pdb=" C LEU X 183 " ideal model delta sigma weight residual 107.69 92.16 15.53 2.01e+00 2.48e-01 5.97e+01 ... (remaining 12685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 4869 17.04 - 34.08: 577 34.08 - 51.12: 145 51.12 - 68.15: 19 68.15 - 85.19: 14 Dihedral angle restraints: 5624 sinusoidal: 2270 harmonic: 3354 Sorted by residual: dihedral pdb=" CA LEU B 128 " pdb=" C LEU B 128 " pdb=" N PRO B 129 " pdb=" CA PRO B 129 " ideal model delta harmonic sigma weight residual 180.00 110.04 69.96 0 5.00e+00 4.00e-02 1.96e+02 dihedral pdb=" N VAL X 178 " pdb=" C VAL X 178 " pdb=" CA VAL X 178 " pdb=" CB VAL X 178 " ideal model delta harmonic sigma weight residual 123.40 148.29 -24.89 0 2.50e+00 1.60e-01 9.92e+01 dihedral pdb=" CA LEU C 60 " pdb=" C LEU C 60 " pdb=" N PRO C 61 " pdb=" CA PRO C 61 " ideal model delta harmonic sigma weight residual 180.00 132.37 47.63 0 5.00e+00 4.00e-02 9.07e+01 ... (remaining 5621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 1429 0.193 - 0.387: 12 0.387 - 0.580: 2 0.580 - 0.774: 1 0.774 - 0.967: 2 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA VAL X 178 " pdb=" N VAL X 178 " pdb=" C VAL X 178 " pdb=" CB VAL X 178 " both_signs ideal model delta sigma weight residual False 2.44 1.47 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA PHE B 18 " pdb=" N PHE B 18 " pdb=" C PHE B 18 " pdb=" CB PHE B 18 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" CA ASP C 99 " pdb=" N ASP C 99 " pdb=" C ASP C 99 " pdb=" CB ASP C 99 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.66 2.00e-01 2.50e+01 1.07e+01 ... (remaining 1443 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " -0.083 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO C 61 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 128 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO B 129 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 450 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO A 451 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.046 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 9 2.27 - 2.93: 3856 2.93 - 3.58: 12279 3.58 - 4.24: 20972 4.24 - 4.90: 36134 Nonbonded interactions: 73250 Sorted by model distance: nonbonded pdb=" CE1 PHE X 187 " pdb=" O GLU X 192 " model vdw 1.611 3.340 nonbonded pdb=" CD1 PHE X 187 " pdb=" O GLU X 192 " model vdw 1.724 3.340 nonbonded pdb=" O VAL X 263 " pdb=" O VAL X 267 " model vdw 1.760 3.040 nonbonded pdb=" CE1 TYR X 79 " pdb=" NH2 ARG X 235 " model vdw 2.059 3.420 nonbonded pdb=" N GLU C 98 " pdb=" OE1 GLU C 98 " model vdw 2.156 3.120 ... (remaining 73245 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.013 0.735 9396 Z= 0.777 Angle : 1.238 16.828 12690 Z= 0.708 Chirality : 0.076 0.967 1446 Planarity : 0.008 0.123 1599 Dihedral : 16.096 85.193 3450 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.09 % Favored : 89.20 % Rotamer: Outliers : 2.23 % Allowed : 10.55 % Favored : 87.22 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.27 % 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: -5.75 (0.19), residues: 1120 helix: -4.25 (0.12), residues: 377 sheet: -3.34 (0.24), residues: 310 loop : -3.44 (0.25), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 208 TYR 0.025 0.003 TYR X 314 PHE 0.028 0.003 PHE B 68 TRP 0.014 0.002 TRP A 246 HIS 0.011 0.002 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.01333 ( 9396) covalent geometry : angle 1.23827 (12690) hydrogen bonds : bond 0.26878 ( 382) hydrogen bonds : angle 10.24778 ( 1074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.5822 (ptt) cc_final: 0.5545 (ptt) outliers start: 23 outliers final: 11 residues processed: 167 average time/residue: 0.0917 time to fit residues: 21.3408 Evaluate side-chains 114 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain X residue 94 MET Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 218 SER Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 78 HIS A 83 ASN A 135 ASN A 193 GLN A 207 GLN A 254 GLN A 303 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 466 HIS B 94 ASN B 242 GLN B 249 HIS B 256 GLN B 321 GLN C 7 HIS C 269 ASN C 277 GLN X 95 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097739 restraints weight = 14392.604| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.44 r_work: 0.3102 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9396 Z= 0.139 Angle : 0.690 13.527 12690 Z= 0.359 Chirality : 0.043 0.205 1446 Planarity : 0.006 0.088 1599 Dihedral : 6.870 59.270 1246 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.91 % Favored : 90.82 % Rotamer: Outliers : 1.74 % Allowed : 15.49 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.27 % 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: -4.04 (0.21), residues: 1122 helix: -1.89 (0.22), residues: 380 sheet: -2.71 (0.26), residues: 298 loop : -3.19 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 235 TYR 0.011 0.001 TYR X 314 PHE 0.014 0.001 PHE B 18 TRP 0.017 0.001 TRP X 260 HIS 0.004 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9396) covalent geometry : angle 0.69045 (12690) hydrogen bonds : bond 0.03561 ( 382) hydrogen bonds : angle 5.53319 ( 1074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8238 (mttm) cc_final: 0.7889 (mtmm) REVERT: A 156 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 157 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8044 (ttp80) REVERT: A 289 HIS cc_start: 0.8255 (m90) cc_final: 0.7949 (m90) REVERT: B 60 TYR cc_start: 0.8440 (p90) cc_final: 0.7704 (p90) REVERT: B 123 ASN cc_start: 0.8528 (m-40) cc_final: 0.8314 (m110) REVERT: B 173 ASP cc_start: 0.9210 (m-30) cc_final: 0.8920 (m-30) REVERT: B 322 ASP cc_start: 0.8222 (m-30) cc_final: 0.7817 (m-30) REVERT: C 127 ASP cc_start: 0.8844 (t0) cc_final: 0.8584 (t0) REVERT: C 155 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: C 278 THR cc_start: 0.9283 (m) cc_final: 0.9011 (p) REVERT: X 187 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: X 213 LEU cc_start: 0.8722 (tt) cc_final: 0.8438 (mt) REVERT: X 267 VAL cc_start: 0.9186 (m) cc_final: 0.8965 (t) REVERT: X 329 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7386 (tm-30) outliers start: 18 outliers final: 8 residues processed: 140 average time/residue: 0.0800 time to fit residues: 16.2948 Evaluate side-chains 126 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 78 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 90 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS C 156 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100656 restraints weight = 14202.575| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.98 r_work: 0.3057 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9396 Z= 0.107 Angle : 0.625 12.524 12690 Z= 0.322 Chirality : 0.042 0.176 1446 Planarity : 0.005 0.091 1599 Dihedral : 6.067 53.834 1231 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.73 % Favored : 91.00 % Rotamer: Outliers : 1.94 % Allowed : 17.33 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % 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: -2.99 (0.24), residues: 1122 helix: -0.46 (0.26), residues: 380 sheet: -2.30 (0.27), residues: 296 loop : -3.04 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.008 0.001 TYR X 314 PHE 0.017 0.001 PHE A 237 TRP 0.020 0.001 TRP X 260 HIS 0.011 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9396) covalent geometry : angle 0.62508 (12690) hydrogen bonds : bond 0.02925 ( 382) hydrogen bonds : angle 4.91467 ( 1074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8210 (mttm) cc_final: 0.7838 (mtmm) REVERT: A 156 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8365 (p) REVERT: B 60 TYR cc_start: 0.8149 (p90) cc_final: 0.7479 (p90) REVERT: B 115 MET cc_start: 0.8859 (ttp) cc_final: 0.8638 (ttt) REVERT: B 162 MET cc_start: 0.9165 (mmt) cc_final: 0.8570 (mmp) REVERT: B 173 ASP cc_start: 0.9048 (m-30) cc_final: 0.8738 (m-30) REVERT: B 322 ASP cc_start: 0.8158 (m-30) cc_final: 0.7796 (m-30) REVERT: C 127 ASP cc_start: 0.8748 (t0) cc_final: 0.8479 (t0) REVERT: C 155 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: C 278 THR cc_start: 0.9201 (m) cc_final: 0.8940 (p) REVERT: X 80 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.5720 (p90) REVERT: X 183 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6928 (tt) REVERT: X 187 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: X 248 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6753 (tm-30) REVERT: X 260 TRP cc_start: 0.6746 (t60) cc_final: 0.6234 (t60) outliers start: 20 outliers final: 10 residues processed: 144 average time/residue: 0.0781 time to fit residues: 16.4001 Evaluate side-chains 129 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 349 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 82 optimal weight: 0.0770 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN B 242 GLN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.134434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095749 restraints weight = 14508.238| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.91 r_work: 0.2964 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9396 Z= 0.224 Angle : 0.689 10.381 12690 Z= 0.353 Chirality : 0.045 0.169 1446 Planarity : 0.005 0.092 1599 Dihedral : 6.064 57.182 1228 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.73 % Favored : 91.00 % Rotamer: Outliers : 2.42 % Allowed : 18.88 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % 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: -2.78 (0.24), residues: 1122 helix: -0.03 (0.27), residues: 383 sheet: -2.25 (0.27), residues: 302 loop : -3.16 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.012 0.001 TYR X 314 PHE 0.016 0.002 PHE B 18 TRP 0.012 0.001 TRP C 236 HIS 0.009 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 9396) covalent geometry : angle 0.68929 (12690) hydrogen bonds : bond 0.03339 ( 382) hydrogen bonds : angle 4.83436 ( 1074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8187 (mttm) cc_final: 0.7836 (mtmm) REVERT: A 156 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8386 (p) REVERT: B 60 TYR cc_start: 0.8266 (p90) cc_final: 0.7956 (p90) REVERT: B 162 MET cc_start: 0.9302 (mmt) cc_final: 0.8850 (mmp) REVERT: C 127 ASP cc_start: 0.8774 (t0) cc_final: 0.8560 (t0) REVERT: X 80 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.5893 (p90) REVERT: X 183 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7044 (tt) REVERT: X 329 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7367 (tm-30) outliers start: 25 outliers final: 14 residues processed: 130 average time/residue: 0.0801 time to fit residues: 15.2035 Evaluate side-chains 125 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 349 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 100 optimal weight: 0.0070 chunk 76 optimal weight: 0.0970 chunk 54 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101442 restraints weight = 14303.438| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.68 r_work: 0.3072 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9396 Z= 0.104 Angle : 0.601 9.762 12690 Z= 0.308 Chirality : 0.041 0.158 1446 Planarity : 0.005 0.081 1599 Dihedral : 5.593 50.016 1228 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.11 % Favored : 91.71 % Rotamer: Outliers : 2.81 % Allowed : 18.97 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % 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: -2.31 (0.24), residues: 1122 helix: 0.46 (0.28), residues: 383 sheet: -2.01 (0.29), residues: 283 loop : -2.96 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 227 TYR 0.008 0.001 TYR X 314 PHE 0.015 0.001 PHE A 237 TRP 0.016 0.001 TRP X 260 HIS 0.007 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9396) covalent geometry : angle 0.60052 (12690) hydrogen bonds : bond 0.02615 ( 382) hydrogen bonds : angle 4.50479 ( 1074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8267 (mttm) cc_final: 0.7893 (mtmm) REVERT: A 121 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7256 (mmtt) REVERT: A 156 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8280 (p) REVERT: B 60 TYR cc_start: 0.8120 (p90) cc_final: 0.7625 (p90) REVERT: B 162 MET cc_start: 0.9241 (mmt) cc_final: 0.8767 (mmp) REVERT: B 208 GLU cc_start: 0.8005 (pt0) cc_final: 0.7738 (pt0) REVERT: C 127 ASP cc_start: 0.8697 (t0) cc_final: 0.8455 (t0) REVERT: C 278 THR cc_start: 0.9160 (m) cc_final: 0.8927 (p) REVERT: X 80 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6114 (p90) REVERT: X 183 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7251 (tt) REVERT: X 248 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6774 (tm-30) REVERT: X 329 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7224 (tm-30) outliers start: 29 outliers final: 14 residues processed: 141 average time/residue: 0.0789 time to fit residues: 16.1920 Evaluate side-chains 124 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.138018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097903 restraints weight = 14291.845| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.47 r_work: 0.3089 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9396 Z= 0.123 Angle : 0.618 9.425 12690 Z= 0.314 Chirality : 0.042 0.160 1446 Planarity : 0.005 0.082 1599 Dihedral : 5.481 51.427 1228 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.56 % Favored : 91.27 % Rotamer: Outliers : 2.52 % Allowed : 19.65 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % 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: -2.03 (0.25), residues: 1122 helix: 0.77 (0.28), residues: 386 sheet: -1.78 (0.29), residues: 287 loop : -2.96 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 270 TYR 0.010 0.001 TYR X 314 PHE 0.014 0.001 PHE A 237 TRP 0.021 0.001 TRP X 260 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9396) covalent geometry : angle 0.61759 (12690) hydrogen bonds : bond 0.02680 ( 382) hydrogen bonds : angle 4.41272 ( 1074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8177 (mttm) cc_final: 0.7786 (mtmm) REVERT: A 121 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7160 (mmtt) REVERT: A 126 LYS cc_start: 0.8983 (tppp) cc_final: 0.8618 (tptp) REVERT: A 156 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8344 (p) REVERT: B 60 TYR cc_start: 0.8229 (p90) cc_final: 0.8005 (p90) REVERT: B 162 MET cc_start: 0.9327 (mmt) cc_final: 0.8852 (mmp) REVERT: B 208 GLU cc_start: 0.8165 (pt0) cc_final: 0.7885 (pt0) REVERT: C 127 ASP cc_start: 0.8928 (t0) cc_final: 0.8670 (t0) REVERT: X 80 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6485 (p90) REVERT: X 183 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6739 (tt) REVERT: X 248 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6658 (tm-30) REVERT: X 329 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7728 (tm-30) outliers start: 26 outliers final: 19 residues processed: 128 average time/residue: 0.0788 time to fit residues: 14.6974 Evaluate side-chains 127 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 0.0870 chunk 50 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096783 restraints weight = 14240.764| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.46 r_work: 0.3074 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9396 Z= 0.158 Angle : 0.630 9.084 12690 Z= 0.322 Chirality : 0.043 0.171 1446 Planarity : 0.005 0.082 1599 Dihedral : 5.504 52.535 1228 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 3.00 % Allowed : 19.85 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % 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: -1.92 (0.25), residues: 1122 helix: 0.89 (0.28), residues: 386 sheet: -1.79 (0.28), residues: 319 loop : -2.91 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 235 TYR 0.011 0.001 TYR X 314 PHE 0.014 0.001 PHE A 237 TRP 0.027 0.001 TRP X 260 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9396) covalent geometry : angle 0.62999 (12690) hydrogen bonds : bond 0.02802 ( 382) hydrogen bonds : angle 4.44434 ( 1074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8047 (mttm) cc_final: 0.7718 (mtmm) REVERT: A 121 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7190 (mmtt) REVERT: A 126 LYS cc_start: 0.9016 (tppp) cc_final: 0.8590 (tptp) REVERT: A 156 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8355 (p) REVERT: B 60 TYR cc_start: 0.8255 (p90) cc_final: 0.8019 (p90) REVERT: B 115 MET cc_start: 0.8501 (ttt) cc_final: 0.8135 (ttt) REVERT: B 162 MET cc_start: 0.9344 (mmt) cc_final: 0.8879 (mmp) REVERT: C 127 ASP cc_start: 0.8918 (t0) cc_final: 0.8646 (t0) REVERT: X 80 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6919 (p90) REVERT: X 183 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6786 (tt) REVERT: X 248 GLN cc_start: 0.7005 (tm-30) cc_final: 0.6617 (tm-30) REVERT: X 329 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7783 (tm-30) outliers start: 31 outliers final: 20 residues processed: 128 average time/residue: 0.0796 time to fit residues: 14.8571 Evaluate side-chains 127 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 102 optimal weight: 0.0030 chunk 28 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100439 restraints weight = 14207.590| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.88 r_work: 0.3055 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9396 Z= 0.111 Angle : 0.607 8.529 12690 Z= 0.309 Chirality : 0.042 0.137 1446 Planarity : 0.005 0.077 1599 Dihedral : 5.381 50.480 1228 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.73 % Favored : 91.09 % Rotamer: Outliers : 2.52 % Allowed : 20.62 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % 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: -1.68 (0.25), residues: 1122 helix: 1.09 (0.28), residues: 385 sheet: -1.57 (0.29), residues: 301 loop : -2.83 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 270 TYR 0.008 0.001 TYR X 314 PHE 0.015 0.001 PHE A 237 TRP 0.027 0.001 TRP X 260 HIS 0.003 0.000 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9396) covalent geometry : angle 0.60653 (12690) hydrogen bonds : bond 0.02576 ( 382) hydrogen bonds : angle 4.34692 ( 1074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8095 (mttm) cc_final: 0.7773 (mtmm) REVERT: A 121 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7153 (mmtt) REVERT: A 126 LYS cc_start: 0.8931 (tppp) cc_final: 0.8521 (tptp) REVERT: A 156 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8264 (p) REVERT: B 60 TYR cc_start: 0.8108 (p90) cc_final: 0.7836 (p90) REVERT: B 162 MET cc_start: 0.9275 (mmt) cc_final: 0.8778 (mmp) REVERT: C 127 ASP cc_start: 0.8667 (t0) cc_final: 0.8408 (t0) REVERT: C 278 THR cc_start: 0.9145 (m) cc_final: 0.8935 (p) REVERT: X 80 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6955 (p90) REVERT: X 183 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6800 (tt) REVERT: X 248 GLN cc_start: 0.6882 (tm-30) cc_final: 0.6563 (tm-30) outliers start: 26 outliers final: 20 residues processed: 126 average time/residue: 0.0801 time to fit residues: 14.7949 Evaluate side-chains 129 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 84 optimal weight: 0.0470 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.139131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.101890 restraints weight = 14231.203| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.81 r_work: 0.3051 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9396 Z= 0.111 Angle : 0.610 9.030 12690 Z= 0.308 Chirality : 0.041 0.137 1446 Planarity : 0.004 0.078 1599 Dihedral : 5.309 50.098 1228 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.90 % Allowed : 20.72 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % 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: -1.59 (0.25), residues: 1122 helix: 1.14 (0.28), residues: 391 sheet: -1.51 (0.29), residues: 301 loop : -2.80 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 85 TYR 0.009 0.001 TYR X 314 PHE 0.014 0.001 PHE A 237 TRP 0.028 0.001 TRP X 260 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9396) covalent geometry : angle 0.61049 (12690) hydrogen bonds : bond 0.02547 ( 382) hydrogen bonds : angle 4.29028 ( 1074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8050 (mttm) cc_final: 0.7650 (mtmm) REVERT: A 121 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7173 (mmtt) REVERT: A 156 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8265 (p) REVERT: B 60 TYR cc_start: 0.8102 (p90) cc_final: 0.7857 (p90) REVERT: B 162 MET cc_start: 0.9282 (mmt) cc_final: 0.8792 (mmp) REVERT: C 127 ASP cc_start: 0.8729 (t0) cc_final: 0.8462 (t0) REVERT: X 248 GLN cc_start: 0.6852 (tm-30) cc_final: 0.6548 (tm-30) outliers start: 30 outliers final: 23 residues processed: 133 average time/residue: 0.0806 time to fit residues: 15.6997 Evaluate side-chains 130 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 258 SER Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS C 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.101943 restraints weight = 13748.252| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.64 r_work: 0.3060 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9396 Z= 0.149 Angle : 0.646 12.403 12690 Z= 0.324 Chirality : 0.043 0.137 1446 Planarity : 0.005 0.080 1599 Dihedral : 5.300 51.766 1226 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.18 % Favored : 90.64 % Rotamer: Outliers : 2.61 % Allowed : 21.49 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % 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: -1.55 (0.25), residues: 1122 helix: 1.26 (0.28), residues: 385 sheet: -1.54 (0.29), residues: 306 loop : -2.78 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 120 TYR 0.010 0.001 TYR X 314 PHE 0.014 0.001 PHE A 237 TRP 0.034 0.001 TRP X 260 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9396) covalent geometry : angle 0.64629 (12690) hydrogen bonds : bond 0.02728 ( 382) hydrogen bonds : angle 4.33795 ( 1074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8068 (mttm) cc_final: 0.7761 (mtmm) REVERT: A 121 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7142 (mmtt) REVERT: A 126 LYS cc_start: 0.8910 (tppp) cc_final: 0.8484 (tptp) REVERT: A 156 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8211 (p) REVERT: A 243 GLU cc_start: 0.8795 (tt0) cc_final: 0.8366 (tt0) REVERT: B 60 TYR cc_start: 0.8162 (p90) cc_final: 0.7899 (p90) REVERT: B 162 MET cc_start: 0.9291 (mmt) cc_final: 0.8792 (mmp) REVERT: B 208 GLU cc_start: 0.7784 (pt0) cc_final: 0.7554 (pt0) REVERT: C 127 ASP cc_start: 0.8679 (t0) cc_final: 0.8402 (t0) outliers start: 27 outliers final: 22 residues processed: 124 average time/residue: 0.0787 time to fit residues: 14.2820 Evaluate side-chains 126 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 258 SER Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 77 optimal weight: 0.0050 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104657 restraints weight = 13554.411| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.72 r_work: 0.3081 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9396 Z= 0.104 Angle : 0.621 12.041 12690 Z= 0.312 Chirality : 0.041 0.135 1446 Planarity : 0.004 0.074 1599 Dihedral : 5.181 49.312 1226 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.73 % Favored : 91.09 % Rotamer: Outliers : 2.42 % Allowed : 21.78 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % 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: -1.41 (0.25), residues: 1122 helix: 1.29 (0.28), residues: 386 sheet: -1.37 (0.29), residues: 297 loop : -2.70 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 85 TYR 0.008 0.001 TYR X 314 PHE 0.014 0.001 PHE A 237 TRP 0.032 0.001 TRP X 260 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9396) covalent geometry : angle 0.62102 (12690) hydrogen bonds : bond 0.02508 ( 382) hydrogen bonds : angle 4.24699 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.89 seconds wall clock time: 37 minutes 14.63 seconds (2234.63 seconds total)