Starting phenix.real_space_refine on Sat Dec 28 21:35:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vku_32019/12_2024/7vku_32019_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vku_32019/12_2024/7vku_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_32019/12_2024/7vku_32019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vku_32019/12_2024/7vku_32019.map" model { file = "/net/cci-nas-00/data/ceres_data/7vku_32019/12_2024/7vku_32019_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vku_32019/12_2024/7vku_32019_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.28, per 1000 atoms: 0.57 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: 2.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.95 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: 2.45 Time building geometry restraints manager: 2.52 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: 1.070 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.370 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.980 ------------------------------------------------------------------------------- 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= 0.740 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP A 246 HIS 0.011 0.002 HIS A 78 PHE 0.028 0.003 PHE B 68 TYR 0.025 0.003 TYR X 314 ARG 0.015 0.001 ARG A 208 *********************** 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 : 1.054 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: 0.2342 time to fit residues: 53.7554 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 : 1.123 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9396 Z= 0.177 Angle : 0.687 13.484 12690 Z= 0.357 Chirality : 0.043 0.199 1446 Planarity : 0.006 0.086 1599 Dihedral : 6.857 58.721 1246 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.00 % Favored : 90.73 % Rotamer: Outliers : 1.74 % Allowed : 15.30 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.21), residues: 1122 helix: -1.89 (0.22), residues: 377 sheet: -2.76 (0.26), residues: 298 loop : -3.11 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 260 HIS 0.004 0.001 HIS B 248 PHE 0.013 0.001 PHE B 18 TYR 0.011 0.001 TYR X 314 ARG 0.004 0.000 ARG B 227 *********************** 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 145 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7554 (mttm) cc_final: 0.7318 (mtmm) REVERT: A 156 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.8071 (p) REVERT: A 157 ARG cc_start: 0.7237 (ttp80) cc_final: 0.7021 (ttp80) REVERT: A 291 MET cc_start: 0.7650 (mmm) cc_final: 0.7137 (tpt) REVERT: A 403 VAL cc_start: 0.7897 (t) cc_final: 0.7681 (t) REVERT: B 173 ASP cc_start: 0.8543 (m-30) cc_final: 0.8244 (m-30) REVERT: B 322 ASP cc_start: 0.6880 (m-30) cc_final: 0.6645 (m-30) REVERT: C 155 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6801 (m-80) outliers start: 18 outliers final: 8 residues processed: 139 average time/residue: 0.1915 time to fit residues: 37.8646 Evaluate side-chains 123 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 57 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9396 Z= 0.264 Angle : 0.675 12.471 12690 Z= 0.347 Chirality : 0.043 0.182 1446 Planarity : 0.005 0.095 1599 Dihedral : 6.303 58.180 1231 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.82 % Favored : 90.82 % Rotamer: Outliers : 2.13 % Allowed : 17.33 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.24), residues: 1122 helix: -0.50 (0.26), residues: 381 sheet: -2.44 (0.27), residues: 296 loop : -3.04 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 260 HIS 0.004 0.001 HIS A 352 PHE 0.017 0.002 PHE A 237 TYR 0.010 0.001 TYR X 314 ARG 0.002 0.000 ARG B 151 *********************** 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 137 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7575 (mttm) cc_final: 0.7268 (mtmm) REVERT: A 156 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8070 (p) REVERT: B 162 MET cc_start: 0.8740 (mmt) cc_final: 0.8196 (mmp) REVERT: C 155 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6874 (m-80) REVERT: X 80 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5209 (p90) outliers start: 22 outliers final: 13 residues processed: 131 average time/residue: 0.2088 time to fit residues: 39.5295 Evaluate side-chains 119 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR 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 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 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 101 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS B 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9396 Z= 0.186 Angle : 0.633 11.171 12690 Z= 0.326 Chirality : 0.042 0.161 1446 Planarity : 0.005 0.088 1599 Dihedral : 5.949 55.304 1229 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.23 % Allowed : 18.10 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.24), residues: 1122 helix: 0.08 (0.27), residues: 383 sheet: -2.20 (0.28), residues: 296 loop : -3.00 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 260 HIS 0.003 0.001 HIS A 310 PHE 0.015 0.001 PHE A 237 TYR 0.011 0.001 TYR B 60 ARG 0.004 0.000 ARG A 157 *********************** 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: 23 poor density : 115 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7530 (mttm) cc_final: 0.7296 (mtmm) REVERT: A 121 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7440 (mmtt) REVERT: A 156 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7972 (p) REVERT: B 115 MET cc_start: 0.8069 (ttp) cc_final: 0.7775 (ttt) REVERT: B 162 MET cc_start: 0.8737 (mmt) cc_final: 0.8154 (mmp) REVERT: C 155 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: X 80 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5242 (p90) REVERT: X 183 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6538 (tt) outliers start: 23 outliers final: 12 residues processed: 130 average time/residue: 0.2026 time to fit residues: 37.8245 Evaluate side-chains 121 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN 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 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS 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 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 62 optimal weight: 0.0050 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 0.0060 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.0070 chunk 98 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5830 ------------------------------------------------------------------------------- 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 249 HIS C 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9396 Z= 0.152 Angle : 0.609 10.626 12690 Z= 0.313 Chirality : 0.041 0.166 1446 Planarity : 0.005 0.086 1599 Dihedral : 5.667 52.784 1228 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.42 % Allowed : 19.46 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.25), residues: 1122 helix: 0.46 (0.27), residues: 386 sheet: -2.00 (0.29), residues: 279 loop : -2.96 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 260 HIS 0.009 0.001 HIS B 248 PHE 0.015 0.001 PHE A 237 TYR 0.008 0.001 TYR X 314 ARG 0.003 0.000 ARG A 157 *********************** 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 140 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7575 (mttm) cc_final: 0.7329 (mtmm) REVERT: A 121 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7313 (mmtt) REVERT: A 156 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7903 (p) REVERT: B 26 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7044 (mt0) REVERT: B 115 MET cc_start: 0.7798 (ttp) cc_final: 0.7534 (ttt) REVERT: B 162 MET cc_start: 0.8696 (mmt) cc_final: 0.8257 (mmp) REVERT: X 80 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5559 (p90) REVERT: X 183 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6638 (tt) outliers start: 25 outliers final: 14 residues processed: 132 average time/residue: 0.2097 time to fit residues: 40.2893 Evaluate side-chains 125 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 403 VAL 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 259 LEU 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 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 349 ASN 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 98 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9396 Z= 0.275 Angle : 0.654 9.855 12690 Z= 0.334 Chirality : 0.044 0.184 1446 Planarity : 0.005 0.085 1599 Dihedral : 5.741 55.381 1228 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.71 % Allowed : 20.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.25), residues: 1122 helix: 0.60 (0.28), residues: 386 sheet: -1.99 (0.28), residues: 304 loop : -3.00 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP X 260 HIS 0.009 0.001 HIS B 248 PHE 0.015 0.002 PHE A 237 TYR 0.011 0.001 TYR C 155 ARG 0.004 0.000 ARG A 208 *********************** 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 134 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7350 (mmtt) REVERT: A 156 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.8050 (p) REVERT: A 222 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7099 (t-90) REVERT: B 162 MET cc_start: 0.8759 (mmt) cc_final: 0.8326 (mmp) REVERT: X 80 PHE cc_start: 0.6233 (OUTLIER) cc_final: 0.5822 (p90) REVERT: X 183 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6770 (tt) outliers start: 28 outliers final: 14 residues processed: 125 average time/residue: 0.2125 time to fit residues: 37.7926 Evaluate side-chains 120 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 222 HIS Chi-restraints excluded: chain A residue 370 THR 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 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 259 LEU 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 198 VAL Chi-restraints excluded: chain X residue 349 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 68 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9396 Z= 0.159 Angle : 0.621 9.551 12690 Z= 0.315 Chirality : 0.042 0.140 1446 Planarity : 0.005 0.079 1599 Dihedral : 5.517 50.831 1228 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.73 % Favored : 91.09 % Rotamer: Outliers : 2.61 % Allowed : 20.72 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.25), residues: 1122 helix: 0.92 (0.28), residues: 386 sheet: -1.88 (0.28), residues: 306 loop : -2.89 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP X 260 HIS 0.003 0.000 HIS A 310 PHE 0.015 0.001 PHE A 237 TYR 0.008 0.001 TYR X 314 ARG 0.003 0.000 ARG A 157 *********************** 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 137 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7175 (mmtt) REVERT: A 156 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7948 (p) REVERT: B 26 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7197 (mt0) REVERT: B 162 MET cc_start: 0.8746 (mmt) cc_final: 0.8298 (mmp) REVERT: X 80 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.5970 (p90) outliers start: 27 outliers final: 18 residues processed: 128 average time/residue: 0.1927 time to fit residues: 36.0250 Evaluate side-chains 125 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 297 SER 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 211 LEU 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 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 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.0370 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9396 Z= 0.186 Angle : 0.636 8.780 12690 Z= 0.321 Chirality : 0.042 0.171 1446 Planarity : 0.005 0.081 1599 Dihedral : 5.380 51.593 1226 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.71 % Allowed : 21.10 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.25), residues: 1122 helix: 0.99 (0.28), residues: 386 sheet: -1.74 (0.28), residues: 306 loop : -2.85 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 260 HIS 0.007 0.001 HIS B 249 PHE 0.014 0.001 PHE A 237 TYR 0.010 0.001 TYR X 314 ARG 0.003 0.000 ARG A 157 *********************** 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 136 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7259 (mmtt) REVERT: A 156 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7971 (p) REVERT: B 26 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7312 (mt0) REVERT: B 162 MET cc_start: 0.8757 (mmt) cc_final: 0.8302 (mmp) REVERT: X 80 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.6018 (p90) REVERT: X 321 ASN cc_start: 0.5937 (p0) cc_final: 0.5638 (p0) outliers start: 28 outliers final: 20 residues processed: 128 average time/residue: 0.1954 time to fit residues: 36.6329 Evaluate side-chains 128 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 THR 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 211 LEU 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 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 349 ASN 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: 2.9990 chunk 104 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.0570 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.0050 chunk 107 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 overall best weight: 0.3310 ------------------------------------------------------------------------------- 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 B 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9396 Z= 0.132 Angle : 0.614 9.639 12690 Z= 0.310 Chirality : 0.041 0.157 1446 Planarity : 0.004 0.074 1599 Dihedral : 5.218 49.086 1226 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.47 % Favored : 91.35 % Rotamer: Outliers : 2.42 % Allowed : 21.30 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.25), residues: 1122 helix: 1.08 (0.28), residues: 393 sheet: -1.60 (0.28), residues: 302 loop : -2.76 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP X 260 HIS 0.007 0.001 HIS B 249 PHE 0.015 0.001 PHE A 237 TYR 0.007 0.001 TYR X 314 ARG 0.002 0.000 ARG A 157 *********************** 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 141 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: B 26 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6901 (mt0) REVERT: B 162 MET cc_start: 0.8676 (mmt) cc_final: 0.8236 (mmp) REVERT: B 173 ASP cc_start: 0.8517 (m-30) cc_final: 0.8255 (m-30) REVERT: X 321 ASN cc_start: 0.6046 (p0) cc_final: 0.5488 (p0) outliers start: 25 outliers final: 16 residues processed: 133 average time/residue: 0.1917 time to fit residues: 37.3624 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 : 1.064 ------------------------------------------------------------------------------- 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 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 323 TRP 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 249 HIS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 230 VAL 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 50 optimal weight: 3.9990 chunk 74 optimal weight: 0.0070 chunk 112 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8404 ------------------------------------------------------------------------------- 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 X 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9396 Z= 0.183 Angle : 0.648 10.198 12690 Z= 0.326 Chirality : 0.042 0.175 1446 Planarity : 0.005 0.080 1599 Dihedral : 5.224 50.589 1226 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.65 % Favored : 91.18 % Rotamer: Outliers : 2.03 % Allowed : 21.59 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.25), residues: 1122 helix: 1.24 (0.28), residues: 387 sheet: -1.45 (0.29), residues: 298 loop : -2.71 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP X 260 HIS 0.009 0.001 HIS B 249 PHE 0.014 0.001 PHE A 237 TYR 0.019 0.001 TYR A 177 ARG 0.005 0.000 ARG A 157 ********************** 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 128 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 157 ARG cc_start: 0.7540 (ttp80) cc_final: 0.7228 (ttp-110) REVERT: B 26 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7072 (mt0) REVERT: B 162 MET cc_start: 0.8747 (mmt) cc_final: 0.8294 (mmp) REVERT: X 321 ASN cc_start: 0.5855 (p0) cc_final: 0.5226 (p0) outliers start: 21 outliers final: 18 residues processed: 122 average time/residue: 0.1889 time to fit residues: 33.7482 Evaluate side-chains 127 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 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 297 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 370 THR 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 249 HIS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 349 ASN 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 82 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** X 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.139082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101099 restraints weight = 14110.198| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.82 r_work: 0.3063 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 9396 Z= 0.234 Angle : 0.970 59.193 12690 Z= 0.560 Chirality : 0.042 0.170 1446 Planarity : 0.005 0.079 1599 Dihedral : 5.292 50.607 1226 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.82 % Favored : 91.00 % Rotamer: Outliers : 1.84 % Allowed : 22.17 % Favored : 75.99 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1122 helix: 1.25 (0.28), residues: 387 sheet: -1.47 (0.29), residues: 298 loop : -2.70 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP X 260 HIS 0.088 0.003 HIS B 249 PHE 0.014 0.001 PHE A 237 TYR 0.018 0.001 TYR A 177 ARG 0.003 0.000 ARG A 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1953.83 seconds wall clock time: 36 minutes 54.94 seconds (2214.94 seconds total)