Starting phenix.real_space_refine on Fri Aug 22 20:18:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgk_40458/08_2025/8sgk_40458.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgk_40458/08_2025/8sgk_40458.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 { model { file = "/net/cci-nas-00/data/ceres_data/8sgk_40458/08_2025/8sgk_40458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgk_40458/08_2025/8sgk_40458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sgk_40458/08_2025/8sgk_40458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgk_40458/08_2025/8sgk_40458.map" } resolution = 3.7 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4856 2.51 5 N 1350 2.21 5 O 1394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7622 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3768 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 453} Chain breaks: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 2.28, per 1000 atoms: 0.30 Number of scatterers: 7622 At special positions: 0 Unit cell: (88.596, 93.564, 110.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1394 8.00 N 1350 7.00 C 4856 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 345.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 42.8% alpha, 18.3% 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 11 through 15 removed outlier: 3.917A pdb=" N GLY A 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 27 removed outlier: 3.684A pdb=" N CYS A 24 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU A 25 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 27 " --> pdb=" O CYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 80 through 89 removed outlier: 4.261A pdb=" N ALA A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.576A pdb=" N GLU A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 169 removed outlier: 3.869A pdb=" N GLU A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.833A pdb=" N MET A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 330 removed outlier: 3.953A pdb=" N THR A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 344 removed outlier: 4.111A pdb=" N HIS A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 353 Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.788A pdb=" N MET A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.935A pdb=" N LEU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 484 through 518 removed outlier: 3.835A pdb=" N GLY A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.915A pdb=" N GLY B 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 removed outlier: 3.684A pdb=" N CYS B 24 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU B 25 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 27 " --> pdb=" O CYS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 80 through 89 removed outlier: 4.261A pdb=" N ALA B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.575A pdb=" N GLU B 148 " --> pdb=" O MET B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 169 removed outlier: 3.868A pdb=" N GLU B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 257 through 267 removed outlier: 3.833A pdb=" N MET B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 330 removed outlier: 3.953A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 344 removed outlier: 4.111A pdb=" N HIS B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 353 Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.788A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.935A pdb=" N LEU B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 484 through 518 removed outlier: 3.835A pdb=" N GLY B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 3.633A pdb=" N MET A 54 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR A 43 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET A 54 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU A 41 " --> pdb=" O MET A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203 removed outlier: 5.084A pdb=" N VAL A 186 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS A 177 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA A 188 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP A 284 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL A 279 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 380 removed outlier: 4.340A pdb=" N GLU A 436 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 450 removed outlier: 4.452A pdb=" N VAL A 449 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 474 " --> pdb=" O VAL A 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.634A pdb=" N MET B 54 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR B 43 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N MET B 54 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU B 41 " --> pdb=" O MET B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 203 removed outlier: 5.083A pdb=" N VAL B 186 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS B 177 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 188 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP B 284 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL B 279 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 376 through 380 removed outlier: 4.341A pdb=" N GLU B 436 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 448 through 450 removed outlier: 4.451A pdb=" N VAL B 449 " --> pdb=" O GLU B 474 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B 474 " --> pdb=" O VAL B 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 382 hydrogen bonds defined for protein. 1068 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: 1.23 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1412 1.32 - 1.45: 1902 1.45 - 1.57: 4468 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 7818 Sorted by residual: bond pdb=" CA TRP A 412 " pdb=" CB TRP A 412 " ideal model delta sigma weight residual 1.522 1.535 -0.012 1.75e-02 3.27e+03 5.06e-01 bond pdb=" CA TRP B 412 " pdb=" CB TRP B 412 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.75e-02 3.27e+03 4.60e-01 bond pdb=" CG PRO A 236 " pdb=" CD PRO A 236 " ideal model delta sigma weight residual 1.512 1.494 0.018 2.70e-02 1.37e+03 4.36e-01 bond pdb=" CG PRO B 236 " pdb=" CD PRO B 236 " ideal model delta sigma weight residual 1.512 1.496 0.016 2.70e-02 1.37e+03 3.73e-01 bond pdb=" CB LYS B 476 " pdb=" CG LYS B 476 " ideal model delta sigma weight residual 1.520 1.503 0.017 3.00e-02 1.11e+03 3.28e-01 ... (remaining 7813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 10436 1.42 - 2.83: 199 2.83 - 4.25: 47 4.25 - 5.67: 6 5.67 - 7.09: 10 Bond angle restraints: 10698 Sorted by residual: angle pdb=" CA ARG A 332 " pdb=" CB ARG A 332 " pdb=" CG ARG A 332 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA ARG B 332 " pdb=" CB ARG B 332 " pdb=" CG ARG B 332 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C VAL A 296 " pdb=" N LEU A 297 " pdb=" CA LEU A 297 " ideal model delta sigma weight residual 122.65 118.83 3.82 1.66e+00 3.63e-01 5.29e+00 angle pdb=" C VAL B 296 " pdb=" N LEU B 297 " pdb=" CA LEU B 297 " ideal model delta sigma weight residual 122.65 118.84 3.81 1.66e+00 3.63e-01 5.25e+00 angle pdb=" N GLY A 478 " pdb=" CA GLY A 478 " pdb=" C GLY A 478 " ideal model delta sigma weight residual 113.76 117.67 -3.91 1.80e+00 3.09e-01 4.71e+00 ... (remaining 10693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4029 17.85 - 35.69: 429 35.69 - 53.54: 152 53.54 - 71.39: 40 71.39 - 89.23: 6 Dihedral angle restraints: 4656 sinusoidal: 1846 harmonic: 2810 Sorted by residual: dihedral pdb=" CA ARG B 477 " pdb=" C ARG B 477 " pdb=" N GLY B 478 " pdb=" CA GLY B 478 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ARG A 477 " pdb=" C ARG A 477 " pdb=" N GLY A 478 " pdb=" CA GLY A 478 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA TRP A 412 " pdb=" C TRP A 412 " pdb=" N PRO A 413 " pdb=" CA PRO A 413 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 4653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 696 0.024 - 0.048: 310 0.048 - 0.072: 99 0.072 - 0.095: 53 0.095 - 0.119: 46 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CA ILE A 287 " pdb=" N ILE A 287 " pdb=" C ILE A 287 " pdb=" CB ILE A 287 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA ILE B 287 " pdb=" N ILE B 287 " pdb=" C ILE B 287 " pdb=" CB ILE B 287 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA VAL B 449 " pdb=" N VAL B 449 " pdb=" C VAL B 449 " pdb=" CB VAL B 449 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 1201 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 479 " -0.008 2.00e-02 2.50e+03 1.18e-02 2.79e+00 pdb=" CG TYR A 479 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 479 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 479 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 479 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 479 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 479 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 479 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 479 " 0.008 2.00e-02 2.50e+03 1.17e-02 2.75e+00 pdb=" CG TYR B 479 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 479 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 479 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 479 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 479 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 479 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 479 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 484 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.73e+00 pdb=" N PRO A 485 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " 0.018 5.00e-02 4.00e+02 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1799 2.80 - 3.32: 7185 3.32 - 3.85: 13029 3.85 - 4.37: 14203 4.37 - 4.90: 25152 Nonbonded interactions: 61368 Sorted by model distance: nonbonded pdb=" O ARG A 328 " pdb=" NH1 ARG A 332 " model vdw 2.269 3.120 nonbonded pdb=" O ARG B 328 " pdb=" NH1 ARG B 332 " model vdw 2.269 3.120 nonbonded pdb=" O TRP B 394 " pdb=" OG1 THR B 397 " model vdw 2.287 3.040 nonbonded pdb=" O TRP A 394 " pdb=" OG1 THR A 397 " model vdw 2.288 3.040 nonbonded pdb=" O GLN B 329 " pdb=" NE2 GLN B 329 " model vdw 2.295 3.120 ... (remaining 61363 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 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: 2.880 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.002 0.063 7820 Z= 0.148 Angle : 0.556 7.087 10698 Z= 0.287 Chirality : 0.037 0.119 1204 Planarity : 0.004 0.033 1400 Dihedral : 17.409 89.232 2844 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.26 % Allowed : 26.80 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 0.76 (0.26), residues: 974 helix: 1.38 (0.27), residues: 336 sheet: 1.02 (0.42), residues: 150 loop : -0.23 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 332 TYR 0.028 0.002 TYR A 479 PHE 0.003 0.000 PHE B 469 TRP 0.018 0.001 TRP A 412 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 7818) covalent geometry : angle 0.55608 (10698) hydrogen bonds : bond 0.19876 ( 382) hydrogen bonds : angle 8.36117 ( 1068) Misc. bond : bond 0.06315 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.8524 (tmm) cc_final: 0.8197 (ttp) REVERT: A 332 ARG cc_start: 0.6996 (mmm160) cc_final: 0.6791 (ptp-110) REVERT: B 99 TYR cc_start: 0.8256 (t80) cc_final: 0.8016 (t80) REVERT: B 144 MET cc_start: 0.8513 (tmm) cc_final: 0.8118 (ttp) outliers start: 2 outliers final: 0 residues processed: 79 average time/residue: 0.0736 time to fit residues: 8.1582 Evaluate side-chains 71 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 410 GLN B 57 ASN B 410 GLN B 513 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.138880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.116089 restraints weight = 14910.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.117564 restraints weight = 10572.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.119085 restraints weight = 8896.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.120141 restraints weight = 6891.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.120675 restraints weight = 6462.402| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7820 Z= 0.180 Angle : 0.589 6.675 10698 Z= 0.297 Chirality : 0.041 0.133 1204 Planarity : 0.005 0.030 1400 Dihedral : 5.720 52.998 1110 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.58 % Allowed : 24.61 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 0.86 (0.26), residues: 974 helix: 1.27 (0.27), residues: 350 sheet: 1.50 (0.42), residues: 162 loop : -0.27 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 332 TYR 0.019 0.002 TYR B 216 PHE 0.006 0.001 PHE B 469 TRP 0.013 0.001 TRP B 412 HIS 0.007 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7818) covalent geometry : angle 0.58864 (10698) hydrogen bonds : bond 0.04502 ( 382) hydrogen bonds : angle 6.16813 ( 1068) Misc. bond : bond 0.00095 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 97 average time/residue: 0.0846 time to fit residues: 11.3096 Evaluate side-chains 79 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 349 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 329 GLN A 513 ASN B 57 ASN B 329 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.132056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.105628 restraints weight = 15087.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108981 restraints weight = 11069.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110496 restraints weight = 8150.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110981 restraints weight = 6777.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.111407 restraints weight = 7060.264| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7820 Z= 0.220 Angle : 0.612 6.617 10698 Z= 0.306 Chirality : 0.042 0.135 1204 Planarity : 0.005 0.030 1400 Dihedral : 5.942 51.794 1110 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.61 % Allowed : 24.23 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 0.76 (0.26), residues: 974 helix: 1.36 (0.27), residues: 348 sheet: 1.24 (0.41), residues: 162 loop : -0.39 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.018 0.002 TYR A 479 PHE 0.010 0.001 PHE A 145 TRP 0.011 0.002 TRP B 412 HIS 0.006 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 7818) covalent geometry : angle 0.61209 (10698) hydrogen bonds : bond 0.04621 ( 382) hydrogen bonds : angle 6.09680 ( 1068) Misc. bond : bond 0.00144 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8635 (ttp) cc_final: 0.8412 (ttp) REVERT: B 144 MET cc_start: 0.8613 (ttp) cc_final: 0.8376 (ttp) outliers start: 28 outliers final: 16 residues processed: 97 average time/residue: 0.1051 time to fit residues: 13.4131 Evaluate side-chains 79 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 506 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 513 ASN B 57 ASN B 72 GLN B 513 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.134152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.106889 restraints weight = 15133.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110160 restraints weight = 10347.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.112504 restraints weight = 8015.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.113918 restraints weight = 6697.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.115199 restraints weight = 5933.241| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7820 Z= 0.138 Angle : 0.571 7.328 10698 Z= 0.282 Chirality : 0.040 0.136 1204 Planarity : 0.005 0.032 1400 Dihedral : 5.892 50.997 1110 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.71 % Allowed : 24.61 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 0.81 (0.26), residues: 974 helix: 1.33 (0.27), residues: 350 sheet: 1.67 (0.42), residues: 150 loop : -0.42 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 442 TYR 0.010 0.002 TYR B 216 PHE 0.007 0.001 PHE B 145 TRP 0.009 0.001 TRP B 412 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7818) covalent geometry : angle 0.57074 (10698) hydrogen bonds : bond 0.04126 ( 382) hydrogen bonds : angle 5.82900 ( 1068) Misc. bond : bond 0.00105 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 216 TYR cc_start: 0.8597 (m-80) cc_final: 0.8383 (m-80) outliers start: 21 outliers final: 13 residues processed: 88 average time/residue: 0.0869 time to fit residues: 10.6898 Evaluate side-chains 79 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 349 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 57 ASN B 36 GLN B 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.135353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108525 restraints weight = 15075.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.111928 restraints weight = 10164.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.114364 restraints weight = 7801.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.116093 restraints weight = 6454.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.117275 restraints weight = 5642.018| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7820 Z= 0.116 Angle : 0.533 7.229 10698 Z= 0.264 Chirality : 0.039 0.135 1204 Planarity : 0.004 0.033 1400 Dihedral : 5.753 51.566 1110 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.87 % Allowed : 23.58 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.00 (0.27), residues: 974 helix: 1.56 (0.27), residues: 350 sheet: 1.41 (0.42), residues: 158 loop : -0.26 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 442 TYR 0.017 0.001 TYR A 216 PHE 0.005 0.001 PHE A 372 TRP 0.013 0.001 TRP B 412 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7818) covalent geometry : angle 0.53289 (10698) hydrogen bonds : bond 0.03734 ( 382) hydrogen bonds : angle 5.52068 ( 1068) Misc. bond : bond 0.00065 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7118 (mtm-85) outliers start: 30 outliers final: 21 residues processed: 99 average time/residue: 0.0869 time to fit residues: 11.9779 Evaluate side-chains 87 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 412 TRP Chi-restraints excluded: chain B residue 506 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 72 GLN B 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.135694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108625 restraints weight = 15128.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.111990 restraints weight = 10307.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.114376 restraints weight = 7928.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.115766 restraints weight = 6598.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.117288 restraints weight = 5837.258| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7820 Z= 0.121 Angle : 0.548 8.075 10698 Z= 0.274 Chirality : 0.040 0.143 1204 Planarity : 0.004 0.035 1400 Dihedral : 5.722 51.765 1110 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.74 % Allowed : 23.07 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.07 (0.27), residues: 974 helix: 1.59 (0.27), residues: 350 sheet: 1.43 (0.43), residues: 158 loop : -0.18 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 442 TYR 0.016 0.002 TYR A 216 PHE 0.008 0.001 PHE A 9 TRP 0.011 0.001 TRP A 412 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7818) covalent geometry : angle 0.54796 (10698) hydrogen bonds : bond 0.03741 ( 382) hydrogen bonds : angle 5.51300 ( 1068) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7265 (mtm-85) outliers start: 29 outliers final: 20 residues processed: 93 average time/residue: 0.0893 time to fit residues: 11.2595 Evaluate side-chains 90 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 412 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 57 ASN B 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.135337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108272 restraints weight = 15129.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.111591 restraints weight = 10306.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114037 restraints weight = 7934.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.115731 restraints weight = 6602.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.116776 restraints weight = 5785.830| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7820 Z= 0.129 Angle : 0.549 7.198 10698 Z= 0.273 Chirality : 0.040 0.138 1204 Planarity : 0.005 0.049 1400 Dihedral : 5.677 51.572 1110 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.61 % Allowed : 23.71 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.04 (0.27), residues: 974 helix: 1.62 (0.27), residues: 350 sheet: 0.93 (0.42), residues: 170 loop : -0.08 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.016 0.002 TYR A 216 PHE 0.007 0.001 PHE B 145 TRP 0.011 0.001 TRP A 412 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7818) covalent geometry : angle 0.54884 (10698) hydrogen bonds : bond 0.03734 ( 382) hydrogen bonds : angle 5.48341 ( 1068) Misc. bond : bond 0.00055 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7369 (mtm-85) REVERT: B 216 TYR cc_start: 0.8593 (m-80) cc_final: 0.8383 (m-80) outliers start: 28 outliers final: 23 residues processed: 90 average time/residue: 0.0838 time to fit residues: 10.4078 Evaluate side-chains 91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 412 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.135756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.108384 restraints weight = 15206.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.111727 restraints weight = 10428.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.114209 restraints weight = 8077.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.115827 restraints weight = 6721.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.117068 restraints weight = 5920.366| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7820 Z= 0.126 Angle : 0.539 7.153 10698 Z= 0.268 Chirality : 0.040 0.137 1204 Planarity : 0.004 0.035 1400 Dihedral : 5.670 51.827 1110 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.61 % Allowed : 23.71 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.11 (0.27), residues: 974 helix: 1.71 (0.27), residues: 350 sheet: 0.97 (0.43), residues: 170 loop : -0.06 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.016 0.002 TYR A 307 PHE 0.012 0.001 PHE A 9 TRP 0.010 0.001 TRP A 412 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7818) covalent geometry : angle 0.53909 (10698) hydrogen bonds : bond 0.03692 ( 382) hydrogen bonds : angle 5.43408 ( 1068) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7392 (mtm-85) REVERT: B 216 TYR cc_start: 0.8572 (m-80) cc_final: 0.8349 (m-80) outliers start: 28 outliers final: 24 residues processed: 88 average time/residue: 0.0850 time to fit residues: 10.3488 Evaluate side-chains 91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 412 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.135181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107954 restraints weight = 15117.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.111179 restraints weight = 10371.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.113578 restraints weight = 8072.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115289 restraints weight = 6765.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.116320 restraints weight = 5941.675| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7820 Z= 0.137 Angle : 0.555 9.041 10698 Z= 0.279 Chirality : 0.040 0.135 1204 Planarity : 0.004 0.035 1400 Dihedral : 5.740 51.705 1110 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.48 % Allowed : 24.36 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.08 (0.27), residues: 974 helix: 1.68 (0.27), residues: 348 sheet: 0.92 (0.43), residues: 170 loop : -0.05 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 442 TYR 0.017 0.002 TYR A 307 PHE 0.010 0.001 PHE A 9 TRP 0.010 0.001 TRP A 412 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7818) covalent geometry : angle 0.55451 (10698) hydrogen bonds : bond 0.03800 ( 382) hydrogen bonds : angle 5.48432 ( 1068) Misc. bond : bond 0.00069 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7391 (mtm-85) REVERT: B 216 TYR cc_start: 0.8575 (m-80) cc_final: 0.8363 (m-80) outliers start: 27 outliers final: 23 residues processed: 88 average time/residue: 0.0780 time to fit residues: 9.7354 Evaluate side-chains 90 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 412 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.0060 chunk 59 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 0.0970 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 335 HIS B 57 ASN B 335 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.137205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110293 restraints weight = 15069.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.113662 restraints weight = 10231.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.116163 restraints weight = 7903.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.117765 restraints weight = 6604.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119057 restraints weight = 5841.390| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7820 Z= 0.105 Angle : 0.541 7.775 10698 Z= 0.269 Chirality : 0.040 0.139 1204 Planarity : 0.004 0.035 1400 Dihedral : 5.586 52.009 1110 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.71 % Allowed : 25.39 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.21 (0.27), residues: 974 helix: 1.69 (0.27), residues: 350 sheet: 1.48 (0.44), residues: 158 loop : -0.07 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 442 TYR 0.017 0.002 TYR A 307 PHE 0.008 0.001 PHE B 145 TRP 0.010 0.001 TRP B 412 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7818) covalent geometry : angle 0.54061 (10698) hydrogen bonds : bond 0.03585 ( 382) hydrogen bonds : angle 5.32327 ( 1068) Misc. bond : bond 0.00036 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.8062 (t80) cc_final: 0.7760 (t80) REVERT: A 141 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7924 (ttp80) REVERT: A 222 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7256 (mtm-85) REVERT: B 216 TYR cc_start: 0.8506 (m-80) cc_final: 0.8301 (m-80) outliers start: 21 outliers final: 18 residues processed: 87 average time/residue: 0.0827 time to fit residues: 9.9799 Evaluate side-chains 88 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 412 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 16 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.137220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110217 restraints weight = 15023.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.113489 restraints weight = 10305.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.115969 restraints weight = 7970.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.117767 restraints weight = 6652.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119001 restraints weight = 5805.107| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 7820 Z= 0.162 Angle : 0.923 59.127 10698 Z= 0.543 Chirality : 0.047 0.883 1204 Planarity : 0.004 0.037 1400 Dihedral : 5.621 52.024 1110 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.84 % Allowed : 25.13 % Favored : 72.04 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.17 (0.27), residues: 974 helix: 1.64 (0.27), residues: 350 sheet: 1.49 (0.44), residues: 158 loop : -0.10 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 442 TYR 0.015 0.001 TYR A 307 PHE 0.012 0.001 PHE B 126 TRP 0.010 0.001 TRP B 412 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7818) covalent geometry : angle 0.92260 (10698) hydrogen bonds : bond 0.03628 ( 382) hydrogen bonds : angle 5.32867 ( 1068) Misc. bond : bond 0.00042 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1283.04 seconds wall clock time: 22 minutes 53.18 seconds (1373.18 seconds total)