Starting phenix.real_space_refine on Thu Mar 13 19:48:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vku_32019/03_2025/7vku_32019_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vku_32019/03_2025/7vku_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_2025/7vku_32019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vku_32019/03_2025/7vku_32019.map" model { file = "/net/cci-nas-00/data/ceres_data/7vku_32019/03_2025/7vku_32019_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vku_32019/03_2025/7vku_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-5624/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: 5.35, per 1000 atoms: 0.58 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: 3.86 Conformation dependent library (CDL) restraints added in 1.5 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: 1.02 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: 4.89 Time building geometry restraints manager: 4.41 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: 0.630 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.350 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:4.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- 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 : 1.103 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: 0.2584 time to fit residues: 58.6892 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 : 0.976 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.137130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098109 restraints weight = 14201.799| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.43 r_work: 0.3092 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 1.066 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8201 (mttm) cc_final: 0.7853 (mtmm) REVERT: A 156 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8447 (p) REVERT: A 157 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8047 (ttp80) REVERT: A 289 HIS cc_start: 0.8264 (m90) cc_final: 0.7954 (m90) REVERT: A 291 MET cc_start: 0.9125 (mmm) cc_final: 0.8293 (tpt) REVERT: B 60 TYR cc_start: 0.8439 (p90) cc_final: 0.7733 (p90) REVERT: B 123 ASN cc_start: 0.8528 (m-40) cc_final: 0.8286 (m-40) REVERT: B 173 ASP cc_start: 0.9211 (m-30) cc_final: 0.8898 (m-30) REVERT: B 322 ASP cc_start: 0.8255 (m-30) cc_final: 0.7854 (m-30) REVERT: C 127 ASP cc_start: 0.8853 (t0) cc_final: 0.8601 (t0) REVERT: C 155 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: C 278 THR cc_start: 0.9302 (m) cc_final: 0.9025 (p) REVERT: X 187 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6239 (m-80) REVERT: X 213 LEU cc_start: 0.8756 (tt) cc_final: 0.8471 (mt) REVERT: X 267 VAL cc_start: 0.9189 (m) cc_final: 0.8969 (t) outliers start: 18 outliers final: 8 residues processed: 139 average time/residue: 0.1978 time to fit residues: 39.3867 Evaluate side-chains 124 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 20 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 B 87 GLN B 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.093838 restraints weight = 14465.554| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.42 r_work: 0.3028 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9396 Z= 0.354 Angle : 0.713 11.851 12690 Z= 0.367 Chirality : 0.045 0.193 1446 Planarity : 0.006 0.100 1599 Dihedral : 6.462 61.684 1231 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.18 % Favored : 90.46 % Rotamer: Outliers : 2.52 % Allowed : 17.52 % Favored : 79.96 % 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: -3.18 (0.23), residues: 1122 helix: -0.59 (0.26), residues: 382 sheet: -2.49 (0.27), residues: 302 loop : -3.11 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP X 260 HIS 0.005 0.001 HIS A 352 PHE 0.017 0.002 PHE A 237 TYR 0.012 0.001 TYR B 164 ARG 0.003 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 140 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8197 (mttm) cc_final: 0.7834 (mtmm) REVERT: A 156 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8494 (p) REVERT: B 60 TYR cc_start: 0.8474 (p90) cc_final: 0.7838 (p90) REVERT: B 162 MET cc_start: 0.9316 (mmt) cc_final: 0.8814 (mmp) REVERT: C 155 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: X 80 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.5887 (p90) REVERT: X 248 GLN cc_start: 0.7401 (tm-30) cc_final: 0.6836 (tm-30) REVERT: X 260 TRP cc_start: 0.6976 (t60) cc_final: 0.6429 (t60) outliers start: 26 outliers final: 14 residues processed: 133 average time/residue: 0.1905 time to fit residues: 36.5629 Evaluate side-chains 122 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE 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 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 323 THR 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 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 16 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS B 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.136310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097990 restraints weight = 14271.036| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.90 r_work: 0.3022 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9396 Z= 0.194 Angle : 0.638 11.101 12690 Z= 0.327 Chirality : 0.043 0.163 1446 Planarity : 0.005 0.088 1599 Dihedral : 5.994 57.324 1229 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.00 % Favored : 90.82 % Rotamer: Outliers : 2.23 % Allowed : 18.68 % Favored : 79.09 % 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: -2.69 (0.24), residues: 1122 helix: 0.04 (0.27), residues: 382 sheet: -2.25 (0.28), residues: 295 loop : -3.06 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 236 HIS 0.003 0.001 HIS A 310 PHE 0.019 0.001 PHE A 331 TYR 0.010 0.001 TYR X 314 ARG 0.003 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 134 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8247 (mttm) cc_final: 0.7881 (mtmm) REVERT: A 121 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7252 (mmtt) REVERT: A 156 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8343 (p) REVERT: B 26 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: B 60 TYR cc_start: 0.8266 (p90) cc_final: 0.7702 (p90) REVERT: B 115 MET cc_start: 0.8778 (ttp) cc_final: 0.8483 (ttm) REVERT: B 162 MET cc_start: 0.9265 (mmt) cc_final: 0.8700 (mmp) REVERT: C 278 THR cc_start: 0.9188 (m) cc_final: 0.8977 (p) REVERT: X 80 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.5958 (p90) REVERT: X 183 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7039 (tt) REVERT: X 267 VAL cc_start: 0.9215 (m) cc_final: 0.8993 (t) outliers start: 23 outliers final: 14 residues processed: 127 average time/residue: 0.1831 time to fit residues: 34.1348 Evaluate side-chains 124 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE 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 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 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 194 THR Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.0020 chunk 95 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 ASN ** 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 = 0.3805 r_free = 0.3805 target = 0.138469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.100673 restraints weight = 14279.173| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.84 r_work: 0.3045 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9396 Z= 0.148 Angle : 0.604 10.560 12690 Z= 0.309 Chirality : 0.041 0.152 1446 Planarity : 0.005 0.085 1599 Dihedral : 5.606 53.082 1226 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.65 % Favored : 91.18 % Rotamer: Outliers : 3.10 % Allowed : 18.49 % Favored : 78.41 % 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: -2.33 (0.24), residues: 1122 helix: 0.40 (0.27), residues: 386 sheet: -1.98 (0.29), residues: 279 loop : -2.97 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 260 HIS 0.010 0.001 HIS B 249 PHE 0.016 0.001 PHE A 331 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 145 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8260 (mttm) cc_final: 0.7893 (mtmm) REVERT: A 121 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7204 (mmtt) REVERT: A 156 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8324 (p) REVERT: A 222 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.7996 (t-90) REVERT: B 60 TYR cc_start: 0.8108 (p90) cc_final: 0.7537 (p90) REVERT: B 162 MET cc_start: 0.9255 (mmt) cc_final: 0.8780 (mmp) REVERT: C 278 THR cc_start: 0.9190 (m) cc_final: 0.8968 (p) REVERT: X 80 PHE cc_start: 0.6915 (OUTLIER) cc_final: 0.6011 (p90) REVERT: X 260 TRP cc_start: 0.6819 (t60) cc_final: 0.6500 (t60) REVERT: X 329 GLU cc_start: 0.7750 (tm-30) cc_final: 0.6932 (tm-30) outliers start: 32 outliers final: 20 residues processed: 134 average time/residue: 0.1990 time to fit residues: 38.1558 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 : 0.967 ------------------------------------------------------------------------------- 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 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 123 ASN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 250 ASN 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 187 PHE Chi-restraints excluded: chain X residue 194 THR 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 25 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 68 optimal weight: 0.0670 chunk 106 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.135323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098477 restraints weight = 14217.155| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.75 r_work: 0.2994 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9396 Z= 0.265 Angle : 0.649 9.685 12690 Z= 0.331 Chirality : 0.043 0.152 1446 Planarity : 0.005 0.085 1599 Dihedral : 5.666 55.378 1226 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.18 % Favored : 90.64 % Rotamer: Outliers : 3.19 % Allowed : 19.55 % Favored : 77.25 % 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: -2.24 (0.25), residues: 1122 helix: 0.56 (0.27), residues: 386 sheet: -1.96 (0.28), residues: 305 loop : -3.02 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 260 HIS 0.011 0.001 HIS B 249 PHE 0.015 0.002 PHE A 237 TYR 0.011 0.001 TYR X 314 ARG 0.003 0.000 ARG A 157 *********************** 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 137 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8202 (mttm) cc_final: 0.7870 (mtmm) REVERT: A 121 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7251 (mmtt) REVERT: A 126 LYS cc_start: 0.8970 (tppp) cc_final: 0.8586 (tptp) REVERT: A 156 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8385 (p) REVERT: A 181 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8475 (t) REVERT: A 222 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7687 (t-90) REVERT: B 26 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: B 60 TYR cc_start: 0.8188 (p90) cc_final: 0.7951 (p90) REVERT: B 162 MET cc_start: 0.9293 (mmt) cc_final: 0.8826 (mmp) REVERT: X 80 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6122 (p90) REVERT: X 260 TRP cc_start: 0.6986 (t60) cc_final: 0.6759 (t60) REVERT: X 329 GLU cc_start: 0.7757 (tm-30) cc_final: 0.6974 (tm-30) outliers start: 33 outliers final: 18 residues processed: 126 average time/residue: 0.2025 time to fit residues: 36.8816 Evaluate side-chains 125 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 181 SER Chi-restraints excluded: chain A residue 222 HIS 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 123 ASN 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 259 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 194 THR 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 69 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 103 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 250 ASN ** X 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.138162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.100565 restraints weight = 14320.159| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.81 r_work: 0.3046 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9396 Z= 0.153 Angle : 0.612 9.462 12690 Z= 0.312 Chirality : 0.041 0.142 1446 Planarity : 0.005 0.080 1599 Dihedral : 5.441 52.113 1226 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.65 % Favored : 91.18 % Rotamer: Outliers : 3.00 % Allowed : 20.52 % Favored : 76.48 % 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: -2.00 (0.25), residues: 1122 helix: 0.86 (0.28), residues: 386 sheet: -1.90 (0.28), residues: 303 loop : -2.93 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 236 HIS 0.006 0.001 HIS B 249 PHE 0.015 0.001 PHE A 237 TYR 0.009 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 144 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8062 (mttm) cc_final: 0.7730 (mtmm) REVERT: A 121 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7139 (mmtt) REVERT: A 156 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8317 (p) REVERT: B 60 TYR cc_start: 0.8113 (p90) cc_final: 0.7805 (p90) REVERT: B 162 MET cc_start: 0.9275 (mmt) cc_final: 0.8791 (mmp) REVERT: C 278 THR cc_start: 0.9176 (m) cc_final: 0.8925 (p) REVERT: X 80 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.5923 (p90) REVERT: X 329 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7752 (tm-30) outliers start: 31 outliers final: 20 residues processed: 133 average time/residue: 0.1905 time to fit residues: 36.4960 Evaluate side-chains 130 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 181 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 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 187 PHE Chi-restraints excluded: chain X residue 194 THR 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 34 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 250 ASN ** X 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.094208 restraints weight = 14498.330| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.44 r_work: 0.3040 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3005 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= 0.339 Angle : 0.689 8.648 12690 Z= 0.350 Chirality : 0.045 0.178 1446 Planarity : 0.005 0.087 1599 Dihedral : 5.671 57.585 1226 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.73 % Favored : 91.09 % Rotamer: Outliers : 2.90 % Allowed : 21.39 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (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: -1.97 (0.25), residues: 1122 helix: 0.81 (0.27), residues: 384 sheet: -1.77 (0.28), residues: 317 loop : -2.93 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP X 260 HIS 0.007 0.001 HIS B 249 PHE 0.015 0.002 PHE B 18 TYR 0.014 0.001 TYR X 314 ARG 0.003 0.000 ARG A 208 *********************** 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: 30 poor density : 106 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8079 (mttm) cc_final: 0.7778 (mtmm) REVERT: A 121 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7341 (mmtt) REVERT: A 126 LYS cc_start: 0.9061 (tppp) cc_final: 0.8630 (tptp) REVERT: A 156 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8489 (p) REVERT: B 26 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8693 (tt0) REVERT: B 60 TYR cc_start: 0.8318 (p90) cc_final: 0.7842 (p90) REVERT: B 208 GLU cc_start: 0.8039 (pt0) cc_final: 0.7767 (pt0) REVERT: X 80 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6744 (p90) REVERT: X 307 TYR cc_start: 0.6101 (t80) cc_final: 0.5891 (t80) REVERT: X 329 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7343 (tm-30) outliers start: 30 outliers final: 20 residues processed: 127 average time/residue: 0.1943 time to fit residues: 35.4822 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 : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 297 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 123 ASN 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 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 93 SER Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 258 SER 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 41 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 250 ASN ** X 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.136104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.095787 restraints weight = 14278.345| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.46 r_work: 0.3081 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9396 Z= 0.232 Angle : 0.651 9.074 12690 Z= 0.331 Chirality : 0.043 0.168 1446 Planarity : 0.005 0.080 1599 Dihedral : 5.557 55.373 1226 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.18 % Favored : 90.64 % Rotamer: Outliers : 2.61 % Allowed : 21.78 % Favored : 75.61 % 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: -1.89 (0.25), residues: 1122 helix: 0.96 (0.28), residues: 385 sheet: -1.74 (0.29), residues: 310 loop : -2.95 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP X 260 HIS 0.010 0.001 HIS B 249 PHE 0.015 0.001 PHE A 237 TYR 0.011 0.001 TYR X 314 ARG 0.003 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 137 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8163 (mttm) cc_final: 0.7776 (mtmm) REVERT: A 121 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7324 (mmtt) REVERT: A 126 LYS cc_start: 0.9014 (tppp) cc_final: 0.8590 (tptp) REVERT: A 156 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8489 (p) REVERT: B 60 TYR cc_start: 0.8321 (p90) cc_final: 0.7839 (p90) REVERT: B 162 MET cc_start: 0.9360 (mmt) cc_final: 0.8903 (mmp) REVERT: X 80 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6955 (p90) REVERT: X 307 TYR cc_start: 0.6000 (t80) cc_final: 0.5796 (t80) REVERT: X 329 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7321 (tm-30) outliers start: 27 outliers final: 20 residues processed: 130 average time/residue: 0.1969 time to fit residues: 36.8419 Evaluate side-chains 128 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 297 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 425 THR 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 187 PHE Chi-restraints excluded: chain X residue 194 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN ** X 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.135936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.096015 restraints weight = 14403.909| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.44 r_work: 0.3071 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 9396 Z= 0.321 Angle : 0.948 59.177 12690 Z= 0.538 Chirality : 0.044 0.352 1446 Planarity : 0.005 0.082 1599 Dihedral : 5.553 55.201 1226 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.27 % Favored : 90.55 % Rotamer: Outliers : 2.52 % Allowed : 21.78 % Favored : 75.70 % Cbeta Deviations : 0.09 % 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: -1.85 (0.25), residues: 1122 helix: 1.01 (0.28), residues: 385 sheet: -1.73 (0.28), residues: 313 loop : -2.93 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP X 260 HIS 0.095 0.003 HIS B 249 PHE 0.015 0.001 PHE A 237 TYR 0.011 0.001 TYR X 314 ARG 0.002 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 132 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8115 (mttm) cc_final: 0.7727 (mtmm) REVERT: A 121 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7318 (mmtt) REVERT: A 126 LYS cc_start: 0.9017 (tppp) cc_final: 0.8590 (tptp) REVERT: A 156 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8477 (p) REVERT: B 60 TYR cc_start: 0.8314 (p90) cc_final: 0.7842 (p90) REVERT: B 162 MET cc_start: 0.9354 (mmt) cc_final: 0.8894 (mmp) REVERT: C 171 GLU cc_start: 0.8172 (pp20) cc_final: 0.7971 (pp20) REVERT: X 80 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6873 (p90) REVERT: X 307 TYR cc_start: 0.5981 (t80) cc_final: 0.5771 (t80) REVERT: X 329 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7321 (tm-30) outliers start: 26 outliers final: 23 residues processed: 122 average time/residue: 0.1962 time to fit residues: 34.6285 Evaluate side-chains 131 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 297 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 203 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 316 VAL Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 194 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 67 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 96 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 12 optimal weight: 0.3980 chunk 63 optimal weight: 10.0000 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 250 ASN C 224 GLN ** X 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.138084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100628 restraints weight = 14175.318| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.82 r_work: 0.3030 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 0.039 9396 Z= 0.154 Angle : 0.633 9.825 12690 Z= 0.322 Chirality : 0.042 0.153 1446 Planarity : 0.005 0.078 1599 Dihedral : 5.418 52.405 1226 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.52 % Allowed : 21.88 % Favored : 75.61 % 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: -1.68 (0.25), residues: 1122 helix: 1.15 (0.28), residues: 385 sheet: -1.63 (0.29), residues: 308 loop : -2.86 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP X 260 HIS 0.007 0.001 HIS B 249 PHE 0.015 0.001 PHE A 237 TYR 0.009 0.001 TYR X 314 ARG 0.002 0.000 ARG A 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5017.42 seconds wall clock time: 88 minutes 58.14 seconds (5338.14 seconds total)