Starting phenix.real_space_refine on Sat Dec 28 20:23:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zn5_14801/12_2024/7zn5_14801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zn5_14801/12_2024/7zn5_14801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zn5_14801/12_2024/7zn5_14801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zn5_14801/12_2024/7zn5_14801.map" model { file = "/net/cci-nas-00/data/ceres_data/7zn5_14801/12_2024/7zn5_14801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zn5_14801/12_2024/7zn5_14801.cif" } resolution = 3.7 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= 1.000 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: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 18 5.16 5 C 5500 2.51 5 N 1562 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9046 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3533 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 430, 3525 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 430, 3525 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3601 Chain: "B" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3566 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 972 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Time building chain proxies: 7.28, per 1000 atoms: 0.80 Number of scatterers: 9046 At special positions: 0 Unit cell: (146.685, 98.679, 89.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 97 15.00 O 1869 8.00 N 1562 7.00 C 5500 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: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1636 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 46.8% alpha, 9.6% beta 13 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 15 through 31 removed outlier: 4.267A pdb=" N TYR A 21 " --> pdb=" O TYR A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 52 through 66 removed outlier: 3.580A pdb=" N VAL A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.773A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.700A pdb=" N LEU A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.153A pdb=" N HIS A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 254 through 268 removed outlier: 4.117A pdb=" N HIS A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.927A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 381 removed outlier: 3.870A pdb=" N LYS A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 426 through 429 removed outlier: 3.547A pdb=" N SER A 429 " --> pdb=" O SER A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 450 through 463 Processing helix chain 'B' and resid 15 through 31 removed outlier: 4.349A pdb=" N TYR B 21 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 52 through 67 removed outlier: 3.615A pdb=" N VAL B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.814A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 removed outlier: 3.659A pdb=" N GLY B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.543A pdb=" N VAL B 172 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 190 removed outlier: 4.374A pdb=" N THR B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 254 through 268 removed outlier: 3.976A pdb=" N HIS B 268 " --> pdb=" O TRP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.693A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 382 removed outlier: 3.789A pdb=" N LYS B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 418 Processing helix chain 'B' and resid 450 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.822A pdb=" N PHE A 109 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR A 423 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N LYS A 421 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLY A 442 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR A 423 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 440 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 388 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 175 removed outlier: 6.698A pdb=" N VAL A 239 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP A 276 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR A 241 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL A 194 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N TYR A 240 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY A 196 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR A 195 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE A 219 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 197 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.552A pdb=" N GLY A 225 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.597A pdb=" N GLY B 175 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 239 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASP B 276 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR B 241 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 194 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR B 240 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY B 196 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 387 through 389 removed outlier: 3.874A pdb=" N LEU B 388 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 440 " --> pdb=" O TYR B 423 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR B 423 " --> pdb=" O VAL B 440 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2318 1.34 - 1.45: 2259 1.45 - 1.57: 4657 1.57 - 1.69: 190 1.69 - 1.81: 32 Bond restraints: 9456 Sorted by residual: bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.726 1.544 0.182 2.00e-02 2.50e+03 8.32e+01 bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.18e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C4 LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.464 1.615 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 9451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 13059 2.23 - 4.45: 119 4.45 - 6.68: 28 6.68 - 8.90: 3 8.90 - 11.13: 6 Bond angle restraints: 13215 Sorted by residual: angle pdb=" CA ARG B 138 " pdb=" CB ARG B 138 " pdb=" CG ARG B 138 " ideal model delta sigma weight residual 114.10 121.66 -7.56 2.00e+00 2.50e-01 1.43e+01 angle pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " pdb=" C4 LLP A 309 " ideal model delta sigma weight residual 120.09 108.96 11.13 3.00e+00 1.11e-01 1.38e+01 angle pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " pdb=" C4 LLP B 309 " ideal model delta sigma weight residual 120.09 108.98 11.11 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CE LLP A 309 " pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 119.26 108.86 10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C LEU A 49 " pdb=" N LYS A 50 " pdb=" CA LYS A 50 " ideal model delta sigma weight residual 122.08 127.01 -4.93 1.47e+00 4.63e-01 1.12e+01 ... (remaining 13210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.21: 4923 28.21 - 56.42: 464 56.42 - 84.63: 30 84.63 - 112.84: 2 112.84 - 141.06: 1 Dihedral angle restraints: 5420 sinusoidal: 2863 harmonic: 2557 Sorted by residual: dihedral pdb=" CA ARG A 74 " pdb=" C ARG A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta harmonic sigma weight residual -180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C4' DA D 33 " pdb=" C3' DA D 33 " pdb=" O3' DA D 33 " pdb=" P DA D 34 " ideal model delta sinusoidal sigma weight residual 220.00 78.94 141.06 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" CA PRO A 73 " pdb=" C PRO A 73 " pdb=" N ARG A 74 " pdb=" CA ARG A 74 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1046 0.032 - 0.064: 257 0.064 - 0.096: 92 0.096 - 0.128: 49 0.128 - 0.159: 6 Chirality restraints: 1450 Sorted by residual: chirality pdb=" CA ARG B 138 " pdb=" N ARG B 138 " pdb=" C ARG B 138 " pdb=" CB ARG B 138 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA GLU B 154 " pdb=" N GLU B 154 " pdb=" C GLU B 154 " pdb=" CB GLU B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1447 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " -0.156 2.00e-02 2.50e+03 2.55e-01 6.53e+02 pdb=" NZ LLP A 309 " 0.341 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " 0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " -0.320 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 309 " 0.089 2.00e-02 2.50e+03 8.51e-02 7.24e+01 pdb=" NZ LLP B 309 " -0.091 2.00e-02 2.50e+03 pdb=" C4 LLP B 309 " 0.081 2.00e-02 2.50e+03 pdb=" C4' LLP B 309 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 168 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 169 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.027 5.00e-02 4.00e+02 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 804 2.74 - 3.28: 8566 3.28 - 3.82: 15123 3.82 - 4.36: 16992 4.36 - 4.90: 27837 Nonbonded interactions: 69322 Sorted by model distance: nonbonded pdb=" OG SER A 254 " pdb=" OD1 ASN A 256 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A 162 " pdb=" OE2 GLU A 281 " model vdw 2.249 3.040 nonbonded pdb=" OE1 GLN B 184 " pdb=" OH TYR B 330 " model vdw 2.262 3.040 nonbonded pdb=" O HIS B 145 " pdb=" OG SER B 339 " model vdw 2.265 3.040 nonbonded pdb=" O THR B 131 " pdb=" ND2 ASN B 136 " model vdw 2.302 3.120 ... (remaining 69317 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 442 or resid 444 through 464)) selection = (chain 'B' and (resid 15 through 442 or resid 444 through 464)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 27.270 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.005 0.182 9456 Z= 0.316 Angle : 0.621 11.128 13215 Z= 0.319 Chirality : 0.037 0.159 1450 Planarity : 0.009 0.255 1348 Dihedral : 18.868 141.055 3784 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.13 % Allowed : 0.52 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.18 (0.30), residues: 852 helix: 1.18 (0.28), residues: 374 sheet: 0.15 (0.52), residues: 106 loop : -0.97 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.003 0.001 HIS A 113 PHE 0.011 0.001 PHE A 128 TYR 0.019 0.001 TYR A 82 ARG 0.003 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8787 (pt) cc_final: 0.8579 (mt) REVERT: A 270 ASN cc_start: 0.7690 (t0) cc_final: 0.7390 (t0) REVERT: B 270 ASN cc_start: 0.7313 (t0) cc_final: 0.6887 (t0) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.2520 time to fit residues: 34.0680 Evaluate side-chains 66 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 183 GLN B 53 GLN B 62 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9456 Z= 0.313 Angle : 0.681 7.217 13215 Z= 0.380 Chirality : 0.045 0.163 1450 Planarity : 0.006 0.049 1348 Dihedral : 20.598 138.873 2050 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.35 % Allowed : 7.96 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.25 (0.29), residues: 852 helix: 0.66 (0.26), residues: 380 sheet: -0.38 (0.47), residues: 119 loop : -0.91 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 264 HIS 0.006 0.002 HIS A 110 PHE 0.019 0.003 PHE B 352 TYR 0.025 0.002 TYR B 21 ARG 0.003 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7726 (pt0) REVERT: A 270 ASN cc_start: 0.7835 (t0) cc_final: 0.7364 (t0) REVERT: B 17 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6412 (t80) REVERT: B 62 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5139 (tp40) REVERT: B 70 GLU cc_start: 0.8534 (tp30) cc_final: 0.8143 (pm20) REVERT: B 268 HIS cc_start: 0.7449 (OUTLIER) cc_final: 0.7168 (t-90) REVERT: B 270 ASN cc_start: 0.7442 (t0) cc_final: 0.6999 (t0) outliers start: 18 outliers final: 11 residues processed: 81 average time/residue: 0.2290 time to fit residues: 26.0272 Evaluate side-chains 72 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9456 Z= 0.201 Angle : 0.589 5.320 13215 Z= 0.334 Chirality : 0.041 0.149 1450 Planarity : 0.005 0.050 1348 Dihedral : 20.782 142.408 2050 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.00 % Allowed : 9.40 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.05 (0.29), residues: 852 helix: 0.89 (0.27), residues: 379 sheet: -0.31 (0.48), residues: 115 loop : -0.88 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 264 HIS 0.006 0.001 HIS B 23 PHE 0.010 0.001 PHE A 151 TYR 0.016 0.001 TYR B 17 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 270 ASN cc_start: 0.7775 (t0) cc_final: 0.7261 (t0) REVERT: B 17 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.6297 (t80) REVERT: B 268 HIS cc_start: 0.7266 (OUTLIER) cc_final: 0.7045 (t-90) REVERT: B 270 ASN cc_start: 0.7471 (t0) cc_final: 0.6964 (t0) outliers start: 23 outliers final: 16 residues processed: 82 average time/residue: 0.2484 time to fit residues: 28.3297 Evaluate side-chains 77 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 23 HIS B 62 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9456 Z= 0.209 Angle : 0.587 7.065 13215 Z= 0.334 Chirality : 0.041 0.154 1450 Planarity : 0.005 0.050 1348 Dihedral : 21.002 143.567 2050 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.26 % Allowed : 11.75 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.05 (0.29), residues: 852 helix: 0.95 (0.27), residues: 379 sheet: -0.21 (0.50), residues: 111 loop : -0.81 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 264 HIS 0.006 0.001 HIS B 23 PHE 0.010 0.002 PHE B 352 TYR 0.016 0.001 TYR B 17 ARG 0.002 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7900 (tm-30) REVERT: A 270 ASN cc_start: 0.7763 (t0) cc_final: 0.7222 (t0) REVERT: B 17 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6349 (t80) REVERT: B 70 GLU cc_start: 0.8502 (tp30) cc_final: 0.8044 (pm20) REVERT: B 270 ASN cc_start: 0.7542 (t0) cc_final: 0.7026 (t0) REVERT: B 339 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8133 (t) outliers start: 25 outliers final: 20 residues processed: 77 average time/residue: 0.2277 time to fit residues: 24.8222 Evaluate side-chains 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9456 Z= 0.186 Angle : 0.567 5.731 13215 Z= 0.324 Chirality : 0.040 0.153 1450 Planarity : 0.005 0.050 1348 Dihedral : 21.166 144.506 2050 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.39 % Allowed : 13.19 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.14 (0.29), residues: 852 helix: 1.04 (0.27), residues: 379 sheet: -0.08 (0.50), residues: 112 loop : -0.83 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 264 HIS 0.004 0.001 HIS A 110 PHE 0.014 0.001 PHE B 119 TYR 0.016 0.001 TYR B 17 ARG 0.002 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7900 (tm-30) REVERT: A 270 ASN cc_start: 0.7752 (t0) cc_final: 0.7203 (t0) REVERT: B 17 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6332 (t80) REVERT: B 70 GLU cc_start: 0.8456 (tp30) cc_final: 0.8009 (pm20) REVERT: B 270 ASN cc_start: 0.7538 (t0) cc_final: 0.7033 (t0) REVERT: B 339 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.8133 (t) outliers start: 26 outliers final: 20 residues processed: 78 average time/residue: 0.2191 time to fit residues: 24.1690 Evaluate side-chains 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 0.0370 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9456 Z= 0.202 Angle : 0.567 6.058 13215 Z= 0.324 Chirality : 0.040 0.153 1450 Planarity : 0.005 0.050 1348 Dihedral : 21.222 144.819 2050 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.00 % Allowed : 14.75 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.14 (0.29), residues: 852 helix: 1.04 (0.27), residues: 379 sheet: -0.14 (0.48), residues: 117 loop : -0.80 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS A 110 PHE 0.012 0.002 PHE B 119 TYR 0.016 0.001 TYR B 17 ARG 0.001 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 270 ASN cc_start: 0.7751 (t0) cc_final: 0.7184 (t0) REVERT: B 17 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6383 (t80) REVERT: B 70 GLU cc_start: 0.8458 (tp30) cc_final: 0.8015 (pm20) REVERT: B 270 ASN cc_start: 0.7571 (t0) cc_final: 0.7060 (t0) REVERT: B 339 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.8144 (t) outliers start: 23 outliers final: 19 residues processed: 75 average time/residue: 0.2092 time to fit residues: 22.7128 Evaluate side-chains 78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.0270 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9456 Z= 0.204 Angle : 0.568 6.648 13215 Z= 0.324 Chirality : 0.040 0.153 1450 Planarity : 0.005 0.050 1348 Dihedral : 21.260 144.982 2050 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.52 % Allowed : 14.75 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.14 (0.30), residues: 852 helix: 1.04 (0.27), residues: 379 sheet: -0.17 (0.48), residues: 117 loop : -0.79 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS A 110 PHE 0.011 0.002 PHE A 352 TYR 0.016 0.001 TYR B 17 ARG 0.001 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.907 Fit side-chains REVERT: A 270 ASN cc_start: 0.7740 (t0) cc_final: 0.7230 (t0) REVERT: B 17 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6393 (t80) REVERT: B 70 GLU cc_start: 0.8453 (tp30) cc_final: 0.7975 (pm20) REVERT: B 270 ASN cc_start: 0.7554 (t0) cc_final: 0.7014 (t0) REVERT: B 339 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8148 (t) outliers start: 27 outliers final: 21 residues processed: 77 average time/residue: 0.2229 time to fit residues: 24.4453 Evaluate side-chains 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 0.0870 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9456 Z= 0.181 Angle : 0.563 6.472 13215 Z= 0.322 Chirality : 0.040 0.151 1450 Planarity : 0.005 0.050 1348 Dihedral : 21.354 145.502 2050 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.26 % Allowed : 15.27 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.20 (0.30), residues: 852 helix: 1.14 (0.27), residues: 379 sheet: -0.10 (0.51), residues: 109 loop : -0.82 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.004 0.001 HIS A 110 PHE 0.010 0.001 PHE B 119 TYR 0.016 0.001 TYR B 17 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6763 (pp) REVERT: A 270 ASN cc_start: 0.7757 (t0) cc_final: 0.7206 (t0) REVERT: B 17 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6321 (t80) REVERT: B 70 GLU cc_start: 0.8402 (tp30) cc_final: 0.7939 (pm20) REVERT: B 270 ASN cc_start: 0.7549 (t0) cc_final: 0.7135 (t0) REVERT: B 339 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.8150 (t) outliers start: 25 outliers final: 20 residues processed: 72 average time/residue: 0.2078 time to fit residues: 21.8650 Evaluate side-chains 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9456 Z= 0.188 Angle : 0.562 6.633 13215 Z= 0.321 Chirality : 0.040 0.149 1450 Planarity : 0.005 0.050 1348 Dihedral : 21.416 145.683 2050 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.26 % Allowed : 15.67 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.24 (0.30), residues: 852 helix: 1.14 (0.27), residues: 379 sheet: -0.09 (0.48), residues: 116 loop : -0.78 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.004 0.001 HIS A 110 PHE 0.009 0.001 PHE B 119 TYR 0.016 0.001 TYR B 17 ARG 0.002 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 141 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6743 (pp) REVERT: A 270 ASN cc_start: 0.7740 (t0) cc_final: 0.7188 (t0) REVERT: B 17 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.6294 (t80) REVERT: B 70 GLU cc_start: 0.8396 (tp30) cc_final: 0.7934 (pm20) REVERT: B 270 ASN cc_start: 0.7580 (t0) cc_final: 0.7168 (t0) REVERT: B 339 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.8159 (t) outliers start: 25 outliers final: 20 residues processed: 73 average time/residue: 0.2148 time to fit residues: 22.9007 Evaluate side-chains 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9456 Z= 0.207 Angle : 0.571 7.074 13215 Z= 0.325 Chirality : 0.041 0.174 1450 Planarity : 0.005 0.050 1348 Dihedral : 21.467 145.738 2050 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.39 % Allowed : 15.80 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.16 (0.30), residues: 852 helix: 1.11 (0.27), residues: 379 sheet: -0.17 (0.50), residues: 108 loop : -0.83 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 124 HIS 0.004 0.001 HIS A 110 PHE 0.011 0.002 PHE A 352 TYR 0.016 0.001 TYR B 17 ARG 0.002 0.000 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 141 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6722 (pp) REVERT: A 270 ASN cc_start: 0.7763 (t0) cc_final: 0.7207 (t0) REVERT: B 17 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6326 (t80) REVERT: B 70 GLU cc_start: 0.8422 (tp30) cc_final: 0.7969 (pm20) REVERT: B 270 ASN cc_start: 0.7610 (t0) cc_final: 0.7230 (t0) REVERT: B 339 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8151 (t) outliers start: 26 outliers final: 20 residues processed: 75 average time/residue: 0.2235 time to fit residues: 24.6924 Evaluate side-chains 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.0050 chunk 65 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.129914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093759 restraints weight = 16264.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.096617 restraints weight = 8830.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098588 restraints weight = 5757.136| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9456 Z= 0.196 Angle : 0.565 6.632 13215 Z= 0.322 Chirality : 0.040 0.161 1450 Planarity : 0.005 0.050 1348 Dihedral : 21.561 145.847 2050 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.00 % Allowed : 16.06 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.18 (0.30), residues: 852 helix: 1.14 (0.27), residues: 379 sheet: -0.21 (0.51), residues: 108 loop : -0.81 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.004 0.001 HIS A 110 PHE 0.010 0.001 PHE B 119 TYR 0.017 0.001 TYR B 17 ARG 0.004 0.000 ARG B 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1880.40 seconds wall clock time: 35 minutes 12.17 seconds (2112.17 seconds total)