Starting phenix.real_space_refine on Thu Nov 14 22:36:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgk_40458/11_2024/8sgk_40458.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgk_40458/11_2024/8sgk_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgk_40458/11_2024/8sgk_40458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgk_40458/11_2024/8sgk_40458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgk_40458/11_2024/8sgk_40458.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgk_40458/11_2024/8sgk_40458.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 7.18, per 1000 atoms: 0.94 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: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.87 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: 2.28 Time building geometry restraints manager: 2.11 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: 0.00 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.850 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.120 ------------------------------------------------------------------------------- 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 0.024 7818 Z= 0.149 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (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 TRP 0.018 0.001 TRP A 412 HIS 0.004 0.001 HIS A 335 PHE 0.003 0.000 PHE B 469 TYR 0.028 0.002 TYR A 479 ARG 0.011 0.000 ARG A 332 *********************** 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 : 0.820 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: 0.2070 time to fit residues: 22.7667 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 : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7818 Z= 0.218 Angle : 0.567 6.832 10698 Z= 0.286 Chirality : 0.040 0.134 1204 Planarity : 0.005 0.031 1400 Dihedral : 5.611 53.182 1110 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.68 % Allowed : 26.03 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 974 helix: 1.29 (0.27), residues: 350 sheet: 1.55 (0.42), residues: 162 loop : -0.24 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 412 HIS 0.006 0.001 HIS A 335 PHE 0.005 0.001 PHE B 469 TYR 0.015 0.002 TYR B 216 ARG 0.003 0.000 ARG B 371 *********************** 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 96 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 TYR cc_start: 0.8291 (t80) cc_final: 0.8067 (t80) outliers start: 13 outliers final: 5 residues processed: 94 average time/residue: 0.1956 time to fit residues: 25.8072 Evaluate side-chains 80 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 122 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 71 optimal weight: 0.0070 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7818 Z= 0.206 Angle : 0.551 6.895 10698 Z= 0.271 Chirality : 0.040 0.132 1204 Planarity : 0.004 0.032 1400 Dihedral : 5.609 52.489 1110 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.84 % Allowed : 23.84 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 974 helix: 1.49 (0.27), residues: 354 sheet: 1.04 (0.41), residues: 170 loop : -0.17 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 412 HIS 0.006 0.001 HIS A 335 PHE 0.007 0.001 PHE B 145 TYR 0.013 0.002 TYR B 479 ARG 0.003 0.000 ARG A 332 *********************** 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 105 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8501 (ttp) cc_final: 0.8278 (ttp) REVERT: B 99 TYR cc_start: 0.8268 (t80) cc_final: 0.8026 (t80) outliers start: 22 outliers final: 8 residues processed: 103 average time/residue: 0.2342 time to fit residues: 31.9687 Evaluate side-chains 80 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 273 LEU 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 273 LEU Chi-restraints excluded: chain B residue 349 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7818 Z= 0.212 Angle : 0.546 6.927 10698 Z= 0.273 Chirality : 0.040 0.132 1204 Planarity : 0.004 0.031 1400 Dihedral : 5.662 52.387 1110 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.22 % Allowed : 23.20 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 974 helix: 1.50 (0.27), residues: 354 sheet: 0.99 (0.40), residues: 170 loop : -0.15 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 483 HIS 0.007 0.001 HIS A 335 PHE 0.006 0.001 PHE A 372 TYR 0.014 0.002 TYR A 479 ARG 0.005 0.000 ARG A 442 *********************** 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 98 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.5572 (OUTLIER) cc_final: 0.5360 (tt0) REVERT: B 279 VAL cc_start: 0.7857 (t) cc_final: 0.7595 (t) outliers start: 25 outliers final: 15 residues processed: 95 average time/residue: 0.1944 time to fit residues: 25.7647 Evaluate side-chains 87 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 72 GLN 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 51 VAL 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 296 VAL 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 53 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 329 GLN B 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 7818 Z= 0.464 Angle : 0.706 6.711 10698 Z= 0.353 Chirality : 0.045 0.136 1204 Planarity : 0.005 0.031 1400 Dihedral : 6.282 56.994 1110 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.22 % Allowed : 23.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 974 helix: 1.24 (0.27), residues: 348 sheet: 0.82 (0.40), residues: 162 loop : -0.50 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 82 HIS 0.007 0.001 HIS B 116 PHE 0.009 0.002 PHE B 469 TYR 0.024 0.003 TYR A 216 ARG 0.007 0.001 ARG B 222 *********************** 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 89 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7398 (mtm-85) outliers start: 25 outliers final: 19 residues processed: 85 average time/residue: 0.1939 time to fit residues: 23.0534 Evaluate side-chains 79 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 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 296 VAL Chi-restraints excluded: chain A residue 349 HIS 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 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 296 VAL Chi-restraints excluded: chain B residue 349 HIS 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 85 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 72 GLN B 513 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7818 Z= 0.275 Angle : 0.591 7.204 10698 Z= 0.294 Chirality : 0.041 0.139 1204 Planarity : 0.005 0.034 1400 Dihedral : 6.173 54.573 1110 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.61 % Allowed : 23.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 974 helix: 1.41 (0.28), residues: 348 sheet: 0.77 (0.41), residues: 162 loop : -0.36 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 412 HIS 0.005 0.001 HIS B 116 PHE 0.009 0.001 PHE A 372 TYR 0.018 0.002 TYR A 216 ARG 0.007 0.001 ARG B 222 *********************** 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 96 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7539 (mtm-85) outliers start: 28 outliers final: 20 residues processed: 89 average time/residue: 0.2047 time to fit residues: 25.5942 Evaluate side-chains 87 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 43 THR 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 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 A residue 412 TRP Chi-restraints excluded: chain B residue 8 PHE 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 296 VAL 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 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 43 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN B 36 GLN B 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7818 Z= 0.188 Angle : 0.545 7.569 10698 Z= 0.269 Chirality : 0.040 0.140 1204 Planarity : 0.004 0.036 1400 Dihedral : 5.991 51.478 1110 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.22 % Allowed : 23.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 974 helix: 1.64 (0.28), residues: 348 sheet: 1.19 (0.41), residues: 156 loop : -0.26 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.004 0.001 HIS A 116 PHE 0.013 0.001 PHE A 61 TYR 0.013 0.002 TYR A 216 ARG 0.005 0.000 ARG B 442 *********************** 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 99 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7490 (mtm-85) outliers start: 25 outliers final: 21 residues processed: 93 average time/residue: 0.2052 time to fit residues: 26.1456 Evaluate side-chains 93 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 B residue 8 PHE 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 296 VAL 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 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.0470 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 90 optimal weight: 0.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7818 Z= 0.174 Angle : 0.557 7.764 10698 Z= 0.275 Chirality : 0.040 0.136 1204 Planarity : 0.005 0.037 1400 Dihedral : 5.834 49.582 1110 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 974 helix: 1.61 (0.28), residues: 348 sheet: 1.05 (0.42), residues: 158 loop : -0.17 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.004 0.001 HIS B 38 PHE 0.007 0.001 PHE A 9 TYR 0.012 0.001 TYR A 216 ARG 0.006 0.000 ARG B 222 *********************** 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 91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ARG cc_start: 0.8254 (ttt90) cc_final: 0.7927 (ttp80) outliers start: 21 outliers final: 18 residues processed: 85 average time/residue: 0.2252 time to fit residues: 26.0844 Evaluate side-chains 81 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 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 412 TRP 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 296 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 82 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 57 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7818 Z= 0.186 Angle : 0.570 9.114 10698 Z= 0.285 Chirality : 0.040 0.141 1204 Planarity : 0.004 0.037 1400 Dihedral : 5.840 49.786 1110 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.22 % Allowed : 23.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 974 helix: 1.60 (0.28), residues: 342 sheet: 0.60 (0.43), residues: 170 loop : 0.21 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 412 HIS 0.004 0.001 HIS B 38 PHE 0.011 0.001 PHE B 145 TYR 0.011 0.001 TYR A 216 ARG 0.007 0.000 ARG B 222 *********************** 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 92 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 86 average time/residue: 0.2105 time to fit residues: 24.8216 Evaluate side-chains 84 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 174 MET 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 B residue 8 PHE Chi-restraints excluded: chain B residue 30 HIS 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 296 VAL 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 93 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7818 Z= 0.179 Angle : 0.559 7.264 10698 Z= 0.276 Chirality : 0.040 0.139 1204 Planarity : 0.004 0.038 1400 Dihedral : 5.791 49.274 1110 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.28), residues: 974 helix: 1.60 (0.27), residues: 342 sheet: 0.67 (0.43), residues: 170 loop : 0.27 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 412 HIS 0.004 0.001 HIS B 38 PHE 0.008 0.001 PHE B 145 TYR 0.013 0.002 TYR B 216 ARG 0.009 0.000 ARG B 222 ********************** 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 88 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8123 (ttp80) outliers start: 21 outliers final: 20 residues processed: 82 average time/residue: 0.1957 time to fit residues: 22.7899 Evaluate side-chains 84 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 174 MET 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 B residue 8 PHE Chi-restraints excluded: chain B residue 30 HIS 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 296 VAL 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 82 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.136512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109108 restraints weight = 15063.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.112536 restraints weight = 10254.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.115055 restraints weight = 7905.439| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 7818 Z= 0.290 Angle : 0.930 59.185 10698 Z= 0.546 Chirality : 0.046 0.797 1204 Planarity : 0.005 0.038 1400 Dihedral : 5.823 49.281 1110 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.58 % Allowed : 25.13 % Favored : 72.29 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 974 helix: 1.56 (0.27), residues: 342 sheet: 0.68 (0.43), residues: 170 loop : 0.24 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 412 HIS 0.004 0.001 HIS B 38 PHE 0.012 0.001 PHE B 126 TYR 0.010 0.001 TYR B 216 ARG 0.006 0.000 ARG B 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.21 seconds wall clock time: 32 minutes 16.42 seconds (1936.42 seconds total)