Starting phenix.real_space_refine on Thu Feb 13 16:53:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vku_32019/02_2025/7vku_32019_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vku_32019/02_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_32019/02_2025/7vku_32019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vku_32019/02_2025/7vku_32019.map" model { file = "/net/cci-nas-00/data/ceres_data/7vku_32019/02_2025/7vku_32019_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vku_32019/02_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-5592/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: 5.45, per 1000 atoms: 0.59 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: 2.34 Conformation dependent library (CDL) restraints added in 1.2 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: 1.03 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: 2.64 Time building geometry restraints manager: 2.69 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: 0.330 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.480 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- 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 : 1.092 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: 0.2278 time to fit residues: 52.4635 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 : 1.156 ------------------------------------------------------------------------------- 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 = 51)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098109 restraints weight = 14201.809| |-----------------------------------------------------------------------------| 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: 0.2946 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 1.023 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8200 (mttm) cc_final: 0.7850 (mtmm) REVERT: A 156 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8449 (p) REVERT: A 157 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8049 (ttp80) REVERT: A 289 HIS cc_start: 0.8268 (m90) cc_final: 0.7958 (m90) REVERT: A 291 MET cc_start: 0.9128 (mmm) cc_final: 0.8298 (tpt) REVERT: B 60 TYR cc_start: 0.8441 (p90) cc_final: 0.7735 (p90) REVERT: B 123 ASN cc_start: 0.8527 (m-40) cc_final: 0.8286 (m-40) REVERT: B 173 ASP cc_start: 0.9211 (m-30) cc_final: 0.8900 (m-30) REVERT: B 322 ASP cc_start: 0.8262 (m-30) cc_final: 0.7857 (m-30) REVERT: C 127 ASP cc_start: 0.8860 (t0) cc_final: 0.8608 (t0) REVERT: C 155 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7635 (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: 0.6238 (m-80) REVERT: X 213 LEU cc_start: 0.8757 (tt) cc_final: 0.8471 (mt) REVERT: X 267 VAL cc_start: 0.9190 (m) cc_final: 0.8970 (t) outliers start: 18 outliers final: 8 residues processed: 139 average time/residue: 0.1945 time to fit residues: 38.6557 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 : 0.993 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS C 156 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.136353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098075 restraints weight = 14346.676| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.97 r_work: 0.3024 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9396 Z= 0.208 Angle : 0.651 12.553 12690 Z= 0.334 Chirality : 0.042 0.178 1446 Planarity : 0.005 0.093 1599 Dihedral : 6.205 57.184 1231 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.91 % Favored : 90.82 % Rotamer: Outliers : 2.13 % Allowed : 17.23 % Favored : 80.64 % 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: -3.01 (0.24), residues: 1122 helix: -0.45 (0.26), residues: 380 sheet: -2.33 (0.27), residues: 296 loop : -3.06 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 260 HIS 0.004 0.001 HIS B 249 PHE 0.017 0.001 PHE A 237 TYR 0.009 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 138 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8226 (mttm) cc_final: 0.7905 (mtmm) REVERT: A 156 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8392 (p) REVERT: B 26 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: B 60 TYR cc_start: 0.8243 (p90) cc_final: 0.7583 (p90) REVERT: B 162 MET cc_start: 0.9230 (mmt) cc_final: 0.8686 (mmp) REVERT: C 127 ASP cc_start: 0.8628 (t0) cc_final: 0.8369 (t0) REVERT: C 155 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: C 278 THR cc_start: 0.9206 (m) cc_final: 0.8953 (p) REVERT: X 80 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5874 (p90) REVERT: X 183 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.6964 (tt) REVERT: X 187 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.5883 (m-80) REVERT: X 248 GLN cc_start: 0.7279 (tm-30) cc_final: 0.6753 (tm-30) REVERT: X 260 TRP cc_start: 0.6789 (t60) cc_final: 0.6274 (t60) outliers start: 22 outliers final: 11 residues processed: 134 average time/residue: 0.2056 time to fit residues: 39.5884 Evaluate side-chains 126 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 420 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 100 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 349 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 248 HIS B 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.134485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094286 restraints weight = 14357.506| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.46 r_work: 0.3042 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9396 Z= 0.319 Angle : 0.680 10.672 12690 Z= 0.348 Chirality : 0.044 0.175 1446 Planarity : 0.005 0.090 1599 Dihedral : 6.131 59.164 1229 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.42 % Allowed : 18.20 % Favored : 79.38 % 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: -2.79 (0.24), residues: 1122 helix: -0.03 (0.27), residues: 383 sheet: -2.32 (0.27), residues: 304 loop : -3.11 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 236 HIS 0.004 0.001 HIS B 249 PHE 0.015 0.002 PHE A 237 TYR 0.012 0.001 TYR X 314 ARG 0.003 0.000 ARG A 208 *********************** 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 140 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8149 (mttm) cc_final: 0.7803 (mtmm) REVERT: A 121 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7304 (mmtt) REVERT: A 156 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8462 (p) REVERT: B 60 TYR cc_start: 0.8376 (p90) cc_final: 0.7814 (p90) REVERT: B 162 MET cc_start: 0.9333 (mmt) cc_final: 0.8794 (mmp) REVERT: C 127 ASP cc_start: 0.8805 (t0) cc_final: 0.8595 (t0) REVERT: X 80 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.5793 (p90) REVERT: X 183 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6921 (tt) REVERT: X 260 TRP cc_start: 0.6851 (t60) cc_final: 0.6524 (t60) outliers start: 25 outliers final: 15 residues processed: 131 average time/residue: 0.2068 time to fit residues: 38.7972 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 : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 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 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 398 LEU 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 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 230 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 48 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 49 optimal weight: 0.0570 chunk 3 optimal weight: 9.9990 chunk 110 optimal weight: 0.1980 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099181 restraints weight = 14273.522| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.04 r_work: 0.3043 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2829 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= 0.150 Angle : 0.605 10.395 12690 Z= 0.312 Chirality : 0.041 0.177 1446 Planarity : 0.005 0.087 1599 Dihedral : 5.737 54.358 1229 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.82 % Favored : 91.00 % Rotamer: Outliers : 2.90 % Allowed : 18.68 % 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: -2.35 (0.25), residues: 1122 helix: 0.42 (0.28), residues: 383 sheet: -2.09 (0.28), residues: 295 loop : -2.95 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 236 HIS 0.014 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 C 270 *********************** 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 141 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8116 (mttm) cc_final: 0.7755 (mtmm) REVERT: A 121 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7268 (mmtt) REVERT: A 156 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8286 (p) REVERT: A 222 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.8074 (t-90) REVERT: B 60 TYR cc_start: 0.8138 (p90) cc_final: 0.7646 (p90) REVERT: B 162 MET cc_start: 0.9250 (mmt) cc_final: 0.8781 (mmp) REVERT: C 127 ASP cc_start: 0.8582 (t0) cc_final: 0.8368 (t0) REVERT: C 278 THR cc_start: 0.9210 (m) cc_final: 0.8951 (p) REVERT: X 80 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.5834 (p90) REVERT: X 183 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7090 (tt) REVERT: X 329 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7308 (tm-30) outliers start: 30 outliers final: 17 residues processed: 129 average time/residue: 0.2012 time to fit residues: 37.1001 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 : 1.086 ------------------------------------------------------------------------------- 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 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 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 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 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 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3795 r_free = 0.3795 target = 0.137698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097635 restraints weight = 14219.724| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.46 r_work: 0.3078 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9396 Z= 0.185 Angle : 0.617 9.915 12690 Z= 0.313 Chirality : 0.042 0.176 1446 Planarity : 0.005 0.082 1599 Dihedral : 5.566 52.657 1228 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.61 % Allowed : 19.55 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % 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: -2.21 (0.25), residues: 1122 helix: 0.63 (0.28), residues: 386 sheet: -1.99 (0.28), residues: 289 loop : -3.00 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 260 HIS 0.007 0.001 HIS B 249 PHE 0.015 0.001 PHE A 237 TYR 0.010 0.001 TYR X 314 ARG 0.001 0.000 ARG C 270 *********************** 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: 27 poor density : 110 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8173 (mttm) cc_final: 0.7844 (mtmm) REVERT: A 121 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7199 (mmtt) REVERT: A 156 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8367 (p) REVERT: B 60 TYR cc_start: 0.8296 (p90) cc_final: 0.8021 (p90) REVERT: B 162 MET cc_start: 0.9323 (mmt) cc_final: 0.8850 (mmp) REVERT: C 127 ASP cc_start: 0.8780 (t0) cc_final: 0.8556 (t0) REVERT: C 278 THR cc_start: 0.9251 (m) cc_final: 0.8945 (p) REVERT: X 80 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6090 (p90) REVERT: X 183 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7244 (tt) REVERT: X 260 TRP cc_start: 0.7045 (t60) cc_final: 0.6741 (t60) REVERT: X 329 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7401 (tm-30) outliers start: 27 outliers final: 16 residues processed: 127 average time/residue: 0.2095 time to fit residues: 37.5712 Evaluate side-chains 123 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 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 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 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 69 optimal weight: 0.0770 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS 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 = 0.3794 r_free = 0.3794 target = 0.137437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.097470 restraints weight = 14340.560| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.46 r_work: 0.3078 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9396 Z= 0.190 Angle : 0.618 9.407 12690 Z= 0.314 Chirality : 0.042 0.142 1446 Planarity : 0.005 0.080 1599 Dihedral : 5.502 52.419 1228 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.09 % Favored : 90.73 % Rotamer: Outliers : 2.61 % Allowed : 20.43 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % 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: -2.03 (0.25), residues: 1122 helix: 0.80 (0.28), residues: 386 sheet: -1.92 (0.28), residues: 303 loop : -2.91 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 260 HIS 0.008 0.001 HIS B 249 PHE 0.014 0.001 PHE A 237 TYR 0.010 0.001 TYR X 314 ARG 0.001 0.000 ARG C 270 *********************** 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 132 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8054 (mttm) cc_final: 0.7723 (mtmm) REVERT: A 121 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7170 (mmtt) REVERT: A 156 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8358 (p) REVERT: B 60 TYR cc_start: 0.8285 (p90) cc_final: 0.8027 (p90) REVERT: B 162 MET cc_start: 0.9331 (mmt) cc_final: 0.8861 (mmp) REVERT: B 208 GLU cc_start: 0.7937 (pt0) cc_final: 0.7642 (pt0) REVERT: C 127 ASP cc_start: 0.8771 (t0) cc_final: 0.8547 (t0) REVERT: X 80 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6060 (p90) REVERT: X 183 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6783 (tt) REVERT: X 260 TRP cc_start: 0.7039 (t60) cc_final: 0.6795 (t60) REVERT: X 329 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7799 (tm-30) outliers start: 27 outliers final: 19 residues processed: 123 average time/residue: 0.1931 time to fit residues: 34.3726 Evaluate side-chains 125 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 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 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 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: 0.8980 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN ** 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 = 0.3772 r_free = 0.3772 target = 0.135603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095326 restraints weight = 14469.110| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.46 r_work: 0.3053 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9396 Z= 0.294 Angle : 0.656 8.656 12690 Z= 0.334 Chirality : 0.044 0.147 1446 Planarity : 0.005 0.084 1599 Dihedral : 5.615 55.129 1228 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.18 % Favored : 90.64 % Rotamer: Outliers : 2.90 % Allowed : 20.91 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % 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: -2.03 (0.25), residues: 1122 helix: 0.80 (0.27), residues: 386 sheet: -1.91 (0.28), residues: 318 loop : -2.93 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 260 HIS 0.012 0.001 HIS B 249 PHE 0.014 0.002 PHE B 18 TYR 0.012 0.001 TYR X 314 ARG 0.003 0.000 ARG X 235 *********************** 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 138 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8082 (mttm) cc_final: 0.7751 (mtmm) REVERT: A 121 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7212 (mmtt) REVERT: A 126 LYS cc_start: 0.9032 (tppp) cc_final: 0.8595 (tptp) REVERT: A 156 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8432 (p) REVERT: B 26 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8690 (tt0) REVERT: B 60 TYR cc_start: 0.8367 (p90) cc_final: 0.7995 (p90) REVERT: B 162 MET cc_start: 0.9359 (mmt) cc_final: 0.8887 (mmp) REVERT: B 208 GLU cc_start: 0.8058 (pt0) cc_final: 0.7776 (pt0) REVERT: X 80 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6052 (p90) REVERT: X 183 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6731 (tt) REVERT: X 329 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7329 (tm-30) outliers start: 30 outliers final: 20 residues processed: 129 average time/residue: 0.1989 time to fit residues: 36.8630 Evaluate side-chains 128 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 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 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 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 GLN B 249 HIS B 250 ASN ** 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 = 0.3798 r_free = 0.3798 target = 0.137680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099461 restraints weight = 14180.354| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.87 r_work: 0.3051 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3185 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= 0.177 Angle : 0.618 9.068 12690 Z= 0.314 Chirality : 0.042 0.138 1446 Planarity : 0.005 0.077 1599 Dihedral : 5.462 51.657 1228 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.81 % Allowed : 21.01 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % 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: -1.74 (0.25), residues: 1122 helix: 1.09 (0.28), residues: 386 sheet: -1.73 (0.28), residues: 307 loop : -2.81 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP X 260 HIS 0.003 0.000 HIS A 310 PHE 0.015 0.001 PHE A 237 TYR 0.009 0.001 TYR X 314 ARG 0.002 0.000 ARG C 166 *********************** 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 134 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8154 (mttm) cc_final: 0.7756 (mtmm) REVERT: A 121 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7238 (mmtt) REVERT: A 126 LYS cc_start: 0.8924 (tppp) cc_final: 0.8527 (tptp) REVERT: A 156 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8343 (p) REVERT: B 60 TYR cc_start: 0.8193 (p90) cc_final: 0.7857 (p90) REVERT: B 162 MET cc_start: 0.9285 (mmt) cc_final: 0.8797 (mmp) REVERT: C 278 THR cc_start: 0.9119 (m) cc_final: 0.8892 (p) REVERT: X 80 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6707 (p90) REVERT: X 183 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6845 (tt) REVERT: X 260 TRP cc_start: 0.6782 (t60) cc_final: 0.6572 (t60) REVERT: X 329 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7560 (tm-30) outliers start: 29 outliers final: 22 residues processed: 125 average time/residue: 0.2005 time to fit residues: 36.2930 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 : 1.100 ------------------------------------------------------------------------------- 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 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 259 LEU 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 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 250 ASN C 224 GLN ** 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 = 0.3808 r_free = 0.3808 target = 0.138596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098609 restraints weight = 14349.295| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.47 r_work: 0.3106 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3315 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= 0.152 Angle : 0.616 9.696 12690 Z= 0.312 Chirality : 0.042 0.135 1446 Planarity : 0.005 0.078 1599 Dihedral : 5.372 50.843 1228 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.52 % Allowed : 21.30 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % 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: -1.56 (0.25), residues: 1122 helix: 1.26 (0.28), residues: 386 sheet: -1.56 (0.29), residues: 301 loop : -2.80 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 260 HIS 0.004 0.001 HIS A 310 PHE 0.015 0.001 PHE A 237 TYR 0.008 0.001 TYR X 314 ARG 0.001 0.000 ARG C 124 ********************** 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 133 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8086 (mttm) cc_final: 0.7696 (mtmm) REVERT: A 121 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7214 (mmtt) REVERT: A 126 LYS cc_start: 0.9016 (tppp) cc_final: 0.8596 (tptp) REVERT: A 156 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8356 (p) REVERT: B 60 TYR cc_start: 0.8253 (p90) cc_final: 0.7991 (p90) REVERT: B 162 MET cc_start: 0.9334 (mmt) cc_final: 0.8861 (mmp) REVERT: C 278 THR cc_start: 0.9199 (m) cc_final: 0.8910 (p) REVERT: X 80 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6464 (p90) REVERT: X 183 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6802 (tt) REVERT: X 321 ASN cc_start: 0.6235 (t0) cc_final: 0.5960 (p0) REVERT: X 329 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7741 (tm-30) outliers start: 26 outliers final: 20 residues processed: 124 average time/residue: 0.1956 time to fit residues: 35.4975 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 : 1.073 ------------------------------------------------------------------------------- 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 323 TRP 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 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 183 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 67 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098300 restraints weight = 14235.769| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.44 r_work: 0.3081 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9396 Z= 0.189 Angle : 0.623 9.590 12690 Z= 0.317 Chirality : 0.042 0.134 1446 Planarity : 0.005 0.079 1599 Dihedral : 5.376 51.736 1228 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.81 % Allowed : 21.59 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % 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: -1.49 (0.25), residues: 1122 helix: 1.34 (0.28), residues: 386 sheet: -1.55 (0.29), residues: 300 loop : -2.76 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP X 260 HIS 0.005 0.001 HIS B 248 PHE 0.014 0.001 PHE A 237 TYR 0.009 0.001 TYR X 314 ARG 0.002 0.000 ARG C 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4675.52 seconds wall clock time: 83 minutes 46.27 seconds (5026.27 seconds total)