Starting phenix.real_space_refine on Fri Jul 3 14:22:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ta2_41126/07_2026/8ta2_41126_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ta2_41126/07_2026/8ta2_41126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ta2_41126/07_2026/8ta2_41126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ta2_41126/07_2026/8ta2_41126.map" model { file = "/net/cci-nas-00/data/ceres_data/8ta2_41126/07_2026/8ta2_41126_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ta2_41126/07_2026/8ta2_41126_trim.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.153 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: 6 Type Number sf(0) Gaussians S 44 5.16 5 Cl 6 4.86 5 C 4774 2.51 5 N 1168 2.21 5 O 1202 1.98 5 H 7411 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14605 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 7231 Classifications: {'peptide': 460} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 437} Chain breaks: 3 Chain: "B" Number of atoms: 7320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7320 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'GH6': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'GH6': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 2.73, per 1000 atoms: 0.19 Number of scatterers: 14605 At special positions: 0 Unit cell: (81.356, 78.518, 118.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 6 17.00 S 44 16.00 O 1202 8.00 N 1168 7.00 C 4774 6.00 H 7411 1.00 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: 1.39 Conformation dependent library (CDL) restraints added in 523.7 milliseconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 1 sheets defined 79.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 88 through 125 removed outlier: 3.580A pdb=" N ILE A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 156 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 204 through 223 Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.654A pdb=" N ALA A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 272 through 296 removed outlier: 3.708A pdb=" N ARG A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 320 through 352 removed outlier: 3.808A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 removed outlier: 3.534A pdb=" N LYS A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.753A pdb=" N ALA A 388 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 430 through 450 removed outlier: 3.589A pdb=" N TRP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 481 removed outlier: 3.658A pdb=" N VAL A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.893A pdb=" N TYR A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.678A pdb=" N PHE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 547 removed outlier: 3.854A pdb=" N SER A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'B' and resid 89 through 126 removed outlier: 3.803A pdb=" N VAL B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 119 " --> pdb=" O CYS B 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 156 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 157 through 160 removed outlier: 3.944A pdb=" N VAL B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 163 through 171 removed outlier: 4.040A pdb=" N THR B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.634A pdb=" N THR B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.518A pdb=" N LYS B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 253 removed outlier: 3.708A pdb=" N ALA B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.090A pdb=" N VAL B 259 " --> pdb=" O PRO B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 296 Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 320 through 352 removed outlier: 3.529A pdb=" N PHE B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 362 Processing helix chain 'B' and resid 364 through 379 removed outlier: 3.806A pdb=" N ALA B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 430 through 450 removed outlier: 3.927A pdb=" N TRP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 481 removed outlier: 3.809A pdb=" N VAL B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 513 removed outlier: 3.949A pdb=" N TYR B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 501 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 502 " --> pdb=" O GLY B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 removed outlier: 3.530A pdb=" N PHE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 546 Processing helix chain 'B' and resid 551 through 561 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 528 hydrogen bonds defined for protein. 1551 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: 3.24 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 7397 1.11 - 1.29: 1070 1.29 - 1.47: 2629 1.47 - 1.64: 3612 1.64 - 1.82: 78 Bond restraints: 14786 Sorted by residual: bond pdb=" N LEU B 472 " pdb=" H LEU B 472 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA B 449 " pdb=" H ALA B 449 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA B 388 " pdb=" H ALA B 388 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LEU B 144 " pdb=" H LEU B 144 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CZ PHE A 316 " pdb=" HZ PHE A 316 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 14781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 23195 2.87 - 5.73: 2761 5.73 - 8.60: 788 8.60 - 11.46: 12 11.46 - 14.33: 13 Bond angle restraints: 26769 Sorted by residual: angle pdb=" CA PHE A 270 " pdb=" CB PHE A 270 " pdb=" CG PHE A 270 " ideal model delta sigma weight residual 113.80 123.19 -9.39 1.00e+00 1.00e+00 8.82e+01 angle pdb=" CA ASP A 402 " pdb=" CB ASP A 402 " pdb=" CG ASP A 402 " ideal model delta sigma weight residual 112.60 118.36 -5.76 1.00e+00 1.00e+00 3.31e+01 angle pdb=" CD ARG B 235 " pdb=" NE ARG B 235 " pdb=" CZ ARG B 235 " ideal model delta sigma weight residual 124.40 132.36 -7.96 1.40e+00 5.10e-01 3.23e+01 angle pdb=" CB HIS B 513 " pdb=" CG HIS B 513 " pdb=" CD2 HIS B 513 " ideal model delta sigma weight residual 131.20 124.14 7.06 1.30e+00 5.92e-01 2.95e+01 angle pdb=" CA PHE B 306 " pdb=" CB PHE B 306 " pdb=" CG PHE B 306 " ideal model delta sigma weight residual 113.80 119.13 -5.33 1.00e+00 1.00e+00 2.84e+01 ... (remaining 26764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6266 17.74 - 35.47: 340 35.47 - 53.21: 148 53.21 - 70.94: 185 70.94 - 88.67: 10 Dihedral angle restraints: 6949 sinusoidal: 3704 harmonic: 3245 Sorted by residual: dihedral pdb=" CA PHE B 222 " pdb=" C PHE B 222 " pdb=" N LEU B 223 " pdb=" CA LEU B 223 " ideal model delta harmonic sigma weight residual 180.00 151.05 28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA GLU B 178 " pdb=" C GLU B 178 " pdb=" N TYR B 179 " pdb=" CA TYR B 179 " ideal model delta harmonic sigma weight residual 180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA LEU B 176 " pdb=" C LEU B 176 " pdb=" N LYS B 177 " pdb=" CA LYS B 177 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 6946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 777 0.082 - 0.164: 310 0.164 - 0.246: 75 0.246 - 0.329: 11 0.329 - 0.411: 2 Chirality restraints: 1175 Sorted by residual: chirality pdb=" CA PRO B 380 " pdb=" N PRO B 380 " pdb=" C PRO B 380 " pdb=" CB PRO B 380 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CA PRO A 380 " pdb=" N PRO A 380 " pdb=" C PRO A 380 " pdb=" CB PRO A 380 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA PRO A 453 " pdb=" N PRO A 453 " pdb=" C PRO A 453 " pdb=" CB PRO A 453 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 1172 not shown) Planarity restraints: 2105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 GH6 B 601 " -0.004 2.00e-02 2.50e+03 7.85e-02 1.54e+02 pdb=" C12 GH6 B 601 " -0.026 2.00e-02 2.50e+03 pdb=" C14 GH6 B 601 " -0.070 2.00e-02 2.50e+03 pdb=" C15 GH6 B 601 " -0.063 2.00e-02 2.50e+03 pdb=" C16 GH6 B 601 " -0.049 2.00e-02 2.50e+03 pdb=" C25 GH6 B 601 " -0.041 2.00e-02 2.50e+03 pdb=" N10 GH6 B 601 " 0.042 2.00e-02 2.50e+03 pdb=" O17 GH6 B 601 " 0.183 2.00e-02 2.50e+03 pdb="CL1 GH6 B 601 " 0.093 2.00e-02 2.50e+03 pdb="CL2 GH6 B 601 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 406 " 0.142 2.00e-02 2.50e+03 6.14e-02 1.51e+02 pdb=" CG TRP A 406 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 406 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 406 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 406 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP A 406 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 406 " -0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 406 " 0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 406 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP A 406 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A 406 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP A 406 " -0.105 2.00e-02 2.50e+03 pdb=" HE3 TRP A 406 " -0.060 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 406 " 0.123 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 406 " -0.046 2.00e-02 2.50e+03 pdb=" HH2 TRP A 406 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 444 " 0.140 2.00e-02 2.50e+03 5.55e-02 1.23e+02 pdb=" CG TRP B 444 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 444 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 444 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 444 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TRP B 444 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 444 " -0.042 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 444 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 444 " -0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP B 444 " 0.033 2.00e-02 2.50e+03 pdb=" HD1 TRP B 444 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP B 444 " -0.083 2.00e-02 2.50e+03 pdb=" HE3 TRP B 444 " -0.071 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 444 " 0.061 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 444 " -0.046 2.00e-02 2.50e+03 pdb=" HH2 TRP B 444 " 0.051 2.00e-02 2.50e+03 ... (remaining 2102 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 779 2.20 - 2.80: 26495 2.80 - 3.40: 41439 3.40 - 4.00: 56050 4.00 - 4.60: 79699 Nonbonded interactions: 204462 Sorted by model distance: nonbonded pdb=" OE1 GLU A 166 " pdb=" HH TYR A 179 " model vdw 1.602 2.450 nonbonded pdb=" OE1 GLU B 166 " pdb=" HH TYR B 179 " model vdw 1.603 2.450 nonbonded pdb=" OE1 GLU B 320 " pdb=" HH TYR B 499 " model vdw 1.610 2.450 nonbonded pdb=" OE2 GLU A 264 " pdb=" HG SER A 516 " model vdw 1.610 2.450 nonbonded pdb=" HG SER A 392 " pdb=" O03 GH6 A 601 " model vdw 1.621 2.450 ... (remaining 204457 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' selection = (chain 'B' and (resid 88 through 297 or resid 304 through 602)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.090 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.110 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 0.095 7375 Z= 0.786 Angle : 1.847 14.326 10033 Z= 1.259 Chirality : 0.091 0.411 1175 Planarity : 0.016 0.145 1230 Dihedral : 13.743 88.674 2571 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.74 % Favored : 97.15 % Rotamer: Outliers : 1.74 % Allowed : 3.88 % Favored : 94.39 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.25), residues: 912 helix: -0.82 (0.17), residues: 694 sheet: None (None), residues: 0 loop : -1.34 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 273 TYR 0.089 0.021 TYR A 134 PHE 0.070 0.013 PHE B 386 TRP 0.088 0.020 TRP A 106 HIS 0.015 0.005 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.01312 / 0.79 ( 7375) covalent geometry : angle 1.84671 / 1.26 (10033) hydrogen bonds : bond 0.21017 / 13.61 ( 528) hydrogen bonds : angle 6.56584 / 4.69 ( 1551) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.7816 (tp) cc_final: 0.7529 (tt) REVERT: A 121 TRP cc_start: 0.8224 (t60) cc_final: 0.7750 (t-100) REVERT: A 122 MET cc_start: 0.8587 (ttm) cc_final: 0.8352 (ttp) REVERT: A 214 MET cc_start: 0.7986 (mtm) cc_final: 0.7783 (mtm) REVERT: A 535 MET cc_start: 0.7441 (mtm) cc_final: 0.7232 (mtp) REVERT: B 183 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6892 (mttp) REVERT: B 200 MET cc_start: 0.7979 (mmp) cc_final: 0.7602 (mmp) REVERT: B 295 TRP cc_start: 0.7100 (t-100) cc_final: 0.6359 (t60) REVERT: B 307 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7183 (pttt) REVERT: B 363 ARG cc_start: 0.6489 (pmt170) cc_final: 0.5911 (pmt-80) REVERT: B 433 LEU cc_start: 0.7691 (tp) cc_final: 0.7397 (tt) REVERT: B 558 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7448 (mtp-110) outliers start: 13 outliers final: 4 residues processed: 120 average time/residue: 1.0763 time to fit residues: 137.8609 Evaluate side-chains 91 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.155990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119734 restraints weight = 20012.956| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.86 r_work: 0.3323 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7375 Z= 0.201 Angle : 0.694 11.621 10033 Z= 0.385 Chirality : 0.040 0.159 1175 Planarity : 0.007 0.066 1230 Dihedral : 8.544 69.225 1016 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.47 % Allowed : 6.42 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.27), residues: 912 helix: 0.85 (0.18), residues: 699 sheet: None (None), residues: 0 loop : -1.66 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 297 TYR 0.018 0.002 TYR A 564 PHE 0.016 0.002 PHE A 270 TRP 0.017 0.001 TRP A 444 HIS 0.007 0.002 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.20 ( 7375) covalent geometry : angle 0.69403 / 0.39 (10033) hydrogen bonds : bond 0.08288 / 5.44 ( 528) hydrogen bonds : angle 4.58733 / 3.33 ( 1551) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.7340 (t60) cc_final: 0.7059 (t60) REVERT: A 321 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7351 (mm) REVERT: A 349 MET cc_start: 0.6433 (ptp) cc_final: 0.5723 (mmt) REVERT: B 183 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5988 (mttp) REVERT: B 295 TRP cc_start: 0.6782 (t-100) cc_final: 0.6568 (t60) REVERT: B 307 LYS cc_start: 0.7254 (ttmt) cc_final: 0.6983 (tttp) REVERT: B 363 ARG cc_start: 0.6243 (pmt170) cc_final: 0.5514 (pmt-80) REVERT: B 433 LEU cc_start: 0.7609 (tp) cc_final: 0.7395 (tt) REVERT: B 561 LYS cc_start: 0.6445 (mttt) cc_final: 0.5718 (mtmt) outliers start: 11 outliers final: 5 residues processed: 101 average time/residue: 1.0574 time to fit residues: 114.1758 Evaluate side-chains 88 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 305 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 50 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.160021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128586 restraints weight = 20588.659| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.60 r_work: 0.3365 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7375 Z= 0.154 Angle : 0.582 11.369 10033 Z= 0.316 Chirality : 0.038 0.132 1175 Planarity : 0.005 0.062 1230 Dihedral : 8.031 69.193 1014 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.47 % Allowed : 7.35 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 912 helix: 1.33 (0.19), residues: 698 sheet: None (None), residues: 0 loop : -1.87 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 471 TYR 0.016 0.002 TYR B 140 PHE 0.015 0.002 PHE A 280 TRP 0.015 0.001 TRP A 444 HIS 0.005 0.002 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 7375) covalent geometry : angle 0.58227 / 0.32 (10033) hydrogen bonds : bond 0.06915 / 4.57 ( 528) hydrogen bonds : angle 4.25615 / 3.12 ( 1551) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.7263 (t60) cc_final: 0.6952 (t60) REVERT: A 313 ASP cc_start: 0.7604 (p0) cc_final: 0.7206 (p0) REVERT: A 314 PHE cc_start: 0.6456 (t80) cc_final: 0.5858 (m-80) REVERT: A 321 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7280 (mm) REVERT: A 349 MET cc_start: 0.6505 (ptp) cc_final: 0.5818 (mmt) REVERT: B 183 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5995 (mttp) REVERT: B 295 TRP cc_start: 0.6615 (t-100) cc_final: 0.6399 (t60) REVERT: B 307 LYS cc_start: 0.7395 (ttmt) cc_final: 0.6978 (pttt) REVERT: B 363 ARG cc_start: 0.6293 (pmt170) cc_final: 0.5425 (pmt-80) REVERT: B 523 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7411 (mt-10) outliers start: 11 outliers final: 6 residues processed: 93 average time/residue: 0.8712 time to fit residues: 87.7781 Evaluate side-chains 88 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.157549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121688 restraints weight = 20047.223| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.85 r_work: 0.3340 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7375 Z= 0.143 Angle : 0.536 11.053 10033 Z= 0.288 Chirality : 0.038 0.123 1175 Planarity : 0.005 0.055 1230 Dihedral : 7.686 68.269 1014 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.94 % Allowed : 8.69 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.28), residues: 912 helix: 1.62 (0.19), residues: 698 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 471 TYR 0.012 0.002 TYR B 140 PHE 0.012 0.001 PHE B 279 TRP 0.013 0.001 TRP A 444 HIS 0.007 0.002 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 7375) covalent geometry : angle 0.53609 / 0.29 (10033) hydrogen bonds : bond 0.06161 / 4.09 ( 528) hydrogen bonds : angle 4.03193 / 2.96 ( 1551) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.7185 (t60) cc_final: 0.6855 (t60) REVERT: A 313 ASP cc_start: 0.7679 (p0) cc_final: 0.7173 (p0) REVERT: A 314 PHE cc_start: 0.6533 (t80) cc_final: 0.5951 (m-80) REVERT: A 349 MET cc_start: 0.6414 (ptp) cc_final: 0.5723 (mmt) REVERT: B 183 LYS cc_start: 0.6116 (OUTLIER) cc_final: 0.5873 (mttp) REVERT: B 295 TRP cc_start: 0.6671 (t-100) cc_final: 0.6413 (t60) REVERT: B 307 LYS cc_start: 0.7396 (ttmt) cc_final: 0.6920 (pttt) REVERT: B 363 ARG cc_start: 0.6354 (pmt170) cc_final: 0.5511 (pmt-80) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.8354 time to fit residues: 84.9909 Evaluate side-chains 89 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 483 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.155431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119117 restraints weight = 20046.888| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.87 r_work: 0.3319 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7375 Z= 0.156 Angle : 0.540 11.113 10033 Z= 0.289 Chirality : 0.038 0.144 1175 Planarity : 0.005 0.056 1230 Dihedral : 7.709 67.522 1014 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.20 % Allowed : 9.76 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.28), residues: 912 helix: 1.67 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -1.89 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 471 TYR 0.013 0.002 TYR B 140 PHE 0.015 0.001 PHE B 279 TRP 0.013 0.001 TRP A 444 HIS 0.005 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 7375) covalent geometry : angle 0.54041 / 0.29 (10033) hydrogen bonds : bond 0.06257 / 4.17 ( 528) hydrogen bonds : angle 3.98969 / 2.93 ( 1551) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8297 (mtp) cc_final: 0.8047 (ttm) REVERT: A 121 TRP cc_start: 0.7165 (t60) cc_final: 0.6820 (t60) REVERT: A 313 ASP cc_start: 0.7768 (p0) cc_final: 0.7417 (p0) REVERT: A 314 PHE cc_start: 0.6594 (t80) cc_final: 0.6055 (m-80) REVERT: A 349 MET cc_start: 0.6301 (ptp) cc_final: 0.5625 (mmt) REVERT: B 183 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5809 (mttp) REVERT: B 295 TRP cc_start: 0.6739 (t-100) cc_final: 0.6472 (t60) REVERT: B 307 LYS cc_start: 0.7453 (ttmt) cc_final: 0.6962 (pttt) REVERT: B 363 ARG cc_start: 0.6281 (pmt170) cc_final: 0.5459 (pmt-80) REVERT: B 386 PHE cc_start: 0.7136 (m-80) cc_final: 0.6902 (m-10) REVERT: B 523 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7530 (mt-10) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.7498 time to fit residues: 75.3983 Evaluate side-chains 89 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 483 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 55 optimal weight: 0.0970 chunk 5 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120901 restraints weight = 20082.552| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.87 r_work: 0.3342 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7375 Z= 0.129 Angle : 0.505 11.121 10033 Z= 0.269 Chirality : 0.037 0.132 1175 Planarity : 0.005 0.052 1230 Dihedral : 7.512 66.591 1014 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.07 % Allowed : 11.63 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.28), residues: 912 helix: 1.91 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -1.77 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 471 TYR 0.013 0.001 TYR B 140 PHE 0.012 0.001 PHE B 279 TRP 0.013 0.001 TRP A 444 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 7375) covalent geometry : angle 0.50537 / 0.27 (10033) hydrogen bonds : bond 0.05650 / 3.77 ( 528) hydrogen bonds : angle 3.88133 / 2.85 ( 1551) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8283 (mtp) cc_final: 0.8021 (ttm) REVERT: A 121 TRP cc_start: 0.7126 (t60) cc_final: 0.6754 (t60) REVERT: A 266 THR cc_start: 0.7969 (p) cc_final: 0.7755 (t) REVERT: A 313 ASP cc_start: 0.7873 (p0) cc_final: 0.7537 (p0) REVERT: A 314 PHE cc_start: 0.6566 (t80) cc_final: 0.5986 (m-80) REVERT: A 349 MET cc_start: 0.6191 (ptp) cc_final: 0.5534 (mmt) REVERT: B 183 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.5729 (mttp) REVERT: B 295 TRP cc_start: 0.6794 (t-100) cc_final: 0.6513 (t60) REVERT: B 307 LYS cc_start: 0.7442 (ttmt) cc_final: 0.6955 (pttt) REVERT: B 347 GLN cc_start: 0.6396 (mt0) cc_final: 0.6094 (tp40) REVERT: B 363 ARG cc_start: 0.6272 (pmt170) cc_final: 0.5449 (pmt-80) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 0.8131 time to fit residues: 81.4582 Evaluate side-chains 89 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117658 restraints weight = 20092.842| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.83 r_work: 0.3295 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7375 Z= 0.201 Angle : 0.582 11.114 10033 Z= 0.313 Chirality : 0.040 0.190 1175 Planarity : 0.006 0.055 1230 Dihedral : 7.849 67.969 1014 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.34 % Allowed : 11.63 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.28), residues: 912 helix: 1.49 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -2.07 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 471 TYR 0.019 0.002 TYR A 499 PHE 0.020 0.002 PHE B 438 TRP 0.012 0.001 TRP B 121 HIS 0.007 0.002 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 ( 7375) covalent geometry : angle 0.58170 / 0.31 (10033) hydrogen bonds : bond 0.06827 / 4.56 ( 528) hydrogen bonds : angle 4.02728 / 2.95 ( 1551) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8370 (mtp) cc_final: 0.8099 (ttm) REVERT: A 121 TRP cc_start: 0.7146 (t60) cc_final: 0.6758 (t60) REVERT: A 313 ASP cc_start: 0.7968 (p0) cc_final: 0.7627 (p0) REVERT: A 314 PHE cc_start: 0.6606 (t80) cc_final: 0.6075 (m-80) REVERT: B 183 LYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5817 (mttp) REVERT: B 295 TRP cc_start: 0.6774 (t-100) cc_final: 0.6517 (t60) REVERT: B 307 LYS cc_start: 0.7505 (ttmt) cc_final: 0.7011 (pttt) REVERT: B 363 ARG cc_start: 0.6237 (pmt170) cc_final: 0.5456 (pmt-80) REVERT: B 523 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7649 (mt-10) outliers start: 10 outliers final: 7 residues processed: 85 average time/residue: 0.8032 time to fit residues: 74.3455 Evaluate side-chains 87 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 483 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 0.0570 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119037 restraints weight = 20113.724| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.85 r_work: 0.3317 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7375 Z= 0.154 Angle : 0.533 11.238 10033 Z= 0.286 Chirality : 0.038 0.151 1175 Planarity : 0.005 0.053 1230 Dihedral : 7.676 66.564 1014 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.34 % Allowed : 12.30 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.28), residues: 912 helix: 1.71 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -1.90 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 471 TYR 0.014 0.002 TYR B 140 PHE 0.014 0.001 PHE B 279 TRP 0.017 0.001 TRP B 121 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 7375) covalent geometry : angle 0.53317 / 0.29 (10033) hydrogen bonds : bond 0.06128 / 4.09 ( 528) hydrogen bonds : angle 3.93545 / 2.89 ( 1551) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8330 (mtp) cc_final: 0.8047 (ttm) REVERT: A 121 TRP cc_start: 0.7136 (t60) cc_final: 0.6746 (t60) REVERT: A 266 THR cc_start: 0.8056 (p) cc_final: 0.7787 (t) REVERT: A 313 ASP cc_start: 0.7971 (p0) cc_final: 0.7598 (p0) REVERT: B 183 LYS cc_start: 0.6077 (OUTLIER) cc_final: 0.5782 (mttp) REVERT: B 295 TRP cc_start: 0.6771 (t-100) cc_final: 0.6533 (t60) REVERT: B 307 LYS cc_start: 0.7492 (ttmt) cc_final: 0.7006 (pttt) REVERT: B 363 ARG cc_start: 0.6288 (pmt170) cc_final: 0.5524 (pmt-80) outliers start: 10 outliers final: 5 residues processed: 88 average time/residue: 0.8036 time to fit residues: 76.8375 Evaluate side-chains 86 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121417 restraints weight = 20102.955| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.86 r_work: 0.3347 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7375 Z= 0.124 Angle : 0.509 11.129 10033 Z= 0.270 Chirality : 0.037 0.153 1175 Planarity : 0.005 0.054 1230 Dihedral : 7.465 67.148 1014 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.94 % Allowed : 13.10 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.28), residues: 912 helix: 2.00 (0.19), residues: 697 sheet: None (None), residues: 0 loop : -1.84 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 471 TYR 0.011 0.001 TYR A 275 PHE 0.011 0.001 PHE A 279 TRP 0.018 0.001 TRP B 121 HIS 0.009 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 7375) covalent geometry : angle 0.50897 / 0.27 (10033) hydrogen bonds : bond 0.05389 / 3.60 ( 528) hydrogen bonds : angle 3.83395 / 2.82 ( 1551) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8303 (mtp) cc_final: 0.8015 (ttm) REVERT: A 121 TRP cc_start: 0.7114 (t60) cc_final: 0.6720 (t60) REVERT: A 266 THR cc_start: 0.8005 (p) cc_final: 0.7779 (t) REVERT: A 313 ASP cc_start: 0.7942 (p0) cc_final: 0.7584 (p0) REVERT: A 349 MET cc_start: 0.6310 (ptp) cc_final: 0.5651 (mmt) REVERT: B 183 LYS cc_start: 0.6002 (OUTLIER) cc_final: 0.5752 (mttm) REVERT: B 295 TRP cc_start: 0.6673 (t-100) cc_final: 0.6432 (t60) REVERT: B 307 LYS cc_start: 0.7431 (ttmt) cc_final: 0.6968 (pttt) REVERT: B 363 ARG cc_start: 0.6352 (pmt170) cc_final: 0.5510 (pmt-80) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.8513 time to fit residues: 81.8886 Evaluate side-chains 87 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN B 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.158402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122649 restraints weight = 19956.532| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.85 r_work: 0.3361 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7375 Z= 0.119 Angle : 0.496 11.064 10033 Z= 0.263 Chirality : 0.037 0.162 1175 Planarity : 0.005 0.052 1230 Dihedral : 7.387 66.125 1014 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.80 % Allowed : 13.37 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.28), residues: 912 helix: 2.11 (0.19), residues: 698 sheet: None (None), residues: 0 loop : -1.75 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 471 TYR 0.011 0.001 TYR B 179 PHE 0.012 0.001 PHE A 279 TRP 0.015 0.001 TRP B 121 HIS 0.008 0.002 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 7375) covalent geometry : angle 0.49634 / 0.26 (10033) hydrogen bonds : bond 0.05173 / 3.46 ( 528) hydrogen bonds : angle 3.77252 / 2.77 ( 1551) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8300 (mtp) cc_final: 0.8006 (ttm) REVERT: A 121 TRP cc_start: 0.7082 (t60) cc_final: 0.6691 (t60) REVERT: A 266 THR cc_start: 0.8013 (p) cc_final: 0.7773 (t) REVERT: A 349 MET cc_start: 0.6296 (ptp) cc_final: 0.5669 (mmt) REVERT: B 183 LYS cc_start: 0.5972 (OUTLIER) cc_final: 0.5710 (mttm) REVERT: B 295 TRP cc_start: 0.6628 (t-100) cc_final: 0.6397 (t60) REVERT: B 307 LYS cc_start: 0.7443 (ttmt) cc_final: 0.6968 (pttt) REVERT: B 363 ARG cc_start: 0.6373 (pmt170) cc_final: 0.5559 (pmt-80) outliers start: 6 outliers final: 3 residues processed: 86 average time/residue: 0.8286 time to fit residues: 77.0938 Evaluate side-chains 85 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN B 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.122115 restraints weight = 20062.394| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.79 r_work: 0.3353 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7375 Z= 0.133 Angle : 0.511 11.116 10033 Z= 0.270 Chirality : 0.037 0.147 1175 Planarity : 0.005 0.053 1230 Dihedral : 7.434 65.311 1014 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.80 % Allowed : 13.50 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.28), residues: 912 helix: 2.02 (0.19), residues: 698 sheet: None (None), residues: 0 loop : -1.79 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 471 TYR 0.010 0.001 TYR B 140 PHE 0.012 0.001 PHE B 279 TRP 0.020 0.001 TRP B 121 HIS 0.005 0.002 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7375) covalent geometry : angle 0.51051 / 0.27 (10033) hydrogen bonds : bond 0.05486 / 3.67 ( 528) hydrogen bonds : angle 3.77647 / 2.78 ( 1551) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4428.36 seconds wall clock time: 75 minutes 51.13 seconds (4551.13 seconds total)