Starting phenix.real_space_refine on Wed Jan 17 20:27:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/01_2024/7lf6_23300.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/01_2024/7lf6_23300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/01_2024/7lf6_23300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/01_2024/7lf6_23300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/01_2024/7lf6_23300.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf6_23300/01_2024/7lf6_23300.pdb" } resolution = 3.5 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= 0.022 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 40 5.16 5 C 4164 2.51 5 N 1016 2.21 5 O 1068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6288 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3144 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3144 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 4.04, per 1000 atoms: 0.64 Number of scatterers: 6288 At special positions: 0 Unit cell: (78.375, 85.8, 81.675, 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 40 16.00 O 1068 8.00 N 1016 7.00 C 4164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.3 seconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.718A pdb=" N PHE A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.070A pdb=" N VAL A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 102 removed outlier: 3.631A pdb=" N VAL A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 133 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.436A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 206 removed outlier: 3.622A pdb=" N HIS A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Proline residue: A 193 - end of helix removed outlier: 3.854A pdb=" N PHE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 removed outlier: 4.486A pdb=" N VAL A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 257 through 284 removed outlier: 4.806A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.676A pdb=" N PHE A 295 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 296 " --> pdb=" O GLU A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 296' Processing helix chain 'A' and resid 298 through 333 removed outlier: 4.412A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 4.286A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.813A pdb=" N ALA A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 396 removed outlier: 3.728A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 437 removed outlier: 5.617A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 444 through 469 Proline residue: A 456 - end of helix removed outlier: 4.787A pdb=" N LEU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU A 461 " --> pdb=" O CYS A 457 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.719A pdb=" N PHE B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.070A pdb=" N VAL B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 102 removed outlier: 3.631A pdb=" N VAL B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 133 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.436A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 206 removed outlier: 3.622A pdb=" N HIS B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix removed outlier: 3.854A pdb=" N PHE B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 223 removed outlier: 4.485A pdb=" N VAL B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 257 through 284 removed outlier: 4.807A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.677A pdb=" N PHE B 295 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 296 " --> pdb=" O GLU B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 296' Processing helix chain 'B' and resid 298 through 333 removed outlier: 4.411A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 4.285A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.813A pdb=" N ALA B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 396 removed outlier: 3.727A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP B 394 " --> pdb=" O GLN B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 437 removed outlier: 5.617A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 444 through 469 Proline residue: B 456 - end of helix removed outlier: 4.787A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU B 461 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1350 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: 1.92 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1932 1.34 - 1.47: 1612 1.47 - 1.60: 2836 1.60 - 1.73: 0 1.73 - 1.85: 62 Bond restraints: 6442 Sorted by residual: bond pdb=" CB CYS B 196 " pdb=" SG CYS B 196 " ideal model delta sigma weight residual 1.808 1.853 -0.045 3.30e-02 9.18e+02 1.86e+00 bond pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " ideal model delta sigma weight residual 1.808 1.852 -0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" CB MET A 130 " pdb=" CG MET A 130 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CB MET B 130 " pdb=" CG MET B 130 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CB TRP B 394 " pdb=" CG TRP B 394 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.83e-01 ... (remaining 6437 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.17: 172 106.17 - 113.14: 3618 113.14 - 120.11: 2377 120.11 - 127.08: 2553 127.08 - 134.06: 72 Bond angle restraints: 8792 Sorted by residual: angle pdb=" N ILE B 218 " pdb=" CA ILE B 218 " pdb=" C ILE B 218 " ideal model delta sigma weight residual 113.42 108.71 4.71 1.17e+00 7.31e-01 1.62e+01 angle pdb=" N ILE A 218 " pdb=" CA ILE A 218 " pdb=" C ILE A 218 " ideal model delta sigma weight residual 113.42 108.73 4.69 1.17e+00 7.31e-01 1.61e+01 angle pdb=" CB MET A 130 " pdb=" CG MET A 130 " pdb=" SD MET A 130 " ideal model delta sigma weight residual 112.70 101.58 11.12 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CB MET B 130 " pdb=" CG MET B 130 " pdb=" SD MET B 130 " ideal model delta sigma weight residual 112.70 101.59 11.11 3.00e+00 1.11e-01 1.37e+01 angle pdb=" N GLN B 361 " pdb=" CA GLN B 361 " pdb=" CB GLN B 361 " ideal model delta sigma weight residual 110.16 114.90 -4.74 1.48e+00 4.57e-01 1.02e+01 ... (remaining 8787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 3356 15.55 - 31.11: 302 31.11 - 46.66: 100 46.66 - 62.21: 10 62.21 - 77.77: 8 Dihedral angle restraints: 3776 sinusoidal: 1392 harmonic: 2384 Sorted by residual: dihedral pdb=" CG ARG A 375 " pdb=" CD ARG A 375 " pdb=" NE ARG A 375 " pdb=" CZ ARG A 375 " ideal model delta sinusoidal sigma weight residual 180.00 135.34 44.66 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG B 375 " pdb=" CD ARG B 375 " pdb=" NE ARG B 375 " pdb=" CZ ARG B 375 " ideal model delta sinusoidal sigma weight residual 180.00 135.40 44.60 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA GLN B 34 " pdb=" C GLN B 34 " pdb=" N ARG B 35 " pdb=" CA ARG B 35 " ideal model delta harmonic sigma weight residual -180.00 -165.41 -14.59 0 5.00e+00 4.00e-02 8.51e+00 ... (remaining 3773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 798 0.047 - 0.095: 237 0.095 - 0.142: 49 0.142 - 0.190: 0 0.190 - 0.237: 2 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CB VAL A 409 " pdb=" CA VAL A 409 " pdb=" CG1 VAL A 409 " pdb=" CG2 VAL A 409 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL B 409 " pdb=" CA VAL B 409 " pdb=" CG1 VAL B 409 " pdb=" CG2 VAL B 409 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL B 455 " pdb=" N VAL B 455 " pdb=" C VAL B 455 " pdb=" CB VAL B 455 " both_signs ideal model delta sigma weight residual False 2.44 2.31 0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1083 not shown) Planarity restraints: 1074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 377 " 0.158 9.50e-02 1.11e+02 7.08e-02 3.24e+00 pdb=" NE ARG B 377 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 377 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 377 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 377 " -0.157 9.50e-02 1.11e+02 7.05e-02 3.22e+00 pdb=" NE ARG A 377 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 377 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 377 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 377 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 192 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO B 193 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 193 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 193 " 0.025 5.00e-02 4.00e+02 ... (remaining 1071 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1028 2.76 - 3.29: 6847 3.29 - 3.83: 11021 3.83 - 4.36: 12361 4.36 - 4.90: 20329 Nonbonded interactions: 51586 Sorted by model distance: nonbonded pdb=" O HIS B 400 " pdb=" OG1 THR B 404 " model vdw 2.220 2.440 nonbonded pdb=" O HIS A 400 " pdb=" OG1 THR A 404 " model vdw 2.220 2.440 nonbonded pdb=" NH2 ARG A 335 " pdb=" O ALA A 402 " model vdw 2.258 2.520 nonbonded pdb=" NH2 ARG B 335 " pdb=" O ALA B 402 " model vdw 2.260 2.520 nonbonded pdb=" O LEU B 213 " pdb=" OG1 THR B 216 " model vdw 2.265 2.440 ... (remaining 51581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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=0.00 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: 1.770 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: 6.660 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.890 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 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 : 0.003 0.045 6442 Z= 0.211 Angle : 0.710 11.116 8792 Z= 0.374 Chirality : 0.045 0.237 1086 Planarity : 0.005 0.071 1074 Dihedral : 13.859 77.767 2214 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.31), residues: 802 helix: 1.06 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -0.41 (0.52), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 324 HIS 0.005 0.001 HIS A 416 PHE 0.018 0.001 PHE A 384 TYR 0.017 0.002 TYR A 313 ARG 0.007 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7516 (mm110) cc_final: 0.7188 (mm110) REVERT: A 262 GLU cc_start: 0.7075 (tp30) cc_final: 0.6673 (tp30) REVERT: A 361 GLN cc_start: 0.6761 (mp10) cc_final: 0.6292 (mp10) REVERT: A 377 ARG cc_start: 0.6352 (tpm170) cc_final: 0.6020 (tpm170) REVERT: A 418 LEU cc_start: 0.8138 (tp) cc_final: 0.7904 (tp) REVERT: A 451 MET cc_start: 0.7219 (ttp) cc_final: 0.6903 (ttp) REVERT: B 38 SER cc_start: 0.7534 (p) cc_final: 0.7288 (p) REVERT: B 71 GLN cc_start: 0.7508 (mm110) cc_final: 0.6852 (mm110) REVERT: B 72 ARG cc_start: 0.7764 (tmt-80) cc_final: 0.7104 (tmt-80) REVERT: B 85 PHE cc_start: 0.8029 (t80) cc_final: 0.7706 (t80) REVERT: B 130 MET cc_start: 0.6429 (mtt) cc_final: 0.6165 (mtt) REVERT: B 188 ILE cc_start: 0.8165 (tt) cc_final: 0.7847 (tt) REVERT: B 357 LEU cc_start: 0.7020 (tt) cc_final: 0.6343 (pp) REVERT: B 361 GLN cc_start: 0.6736 (mp10) cc_final: 0.6230 (mp10) REVERT: B 414 ARG cc_start: 0.7125 (mtt-85) cc_final: 0.6850 (mtt-85) REVERT: B 451 MET cc_start: 0.7030 (ttp) cc_final: 0.6698 (ttp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2462 time to fit residues: 54.2246 Evaluate side-chains 173 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS A 452 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6442 Z= 0.224 Angle : 0.643 11.404 8792 Z= 0.328 Chirality : 0.044 0.216 1086 Planarity : 0.005 0.040 1074 Dihedral : 4.137 16.904 860 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.35 % Allowed : 12.65 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.31), residues: 802 helix: 1.20 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -0.55 (0.53), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.012 0.001 HIS B 449 PHE 0.014 0.001 PHE B 459 TYR 0.019 0.002 TYR B 313 ARG 0.005 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7919 (mp) REVERT: A 71 GLN cc_start: 0.7542 (mm110) cc_final: 0.7180 (mm110) REVERT: A 262 GLU cc_start: 0.7211 (tp30) cc_final: 0.6992 (tp30) REVERT: A 332 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7363 (mm) REVERT: A 357 LEU cc_start: 0.7363 (tt) cc_final: 0.7160 (tt) REVERT: A 377 ARG cc_start: 0.6178 (tpm170) cc_final: 0.5569 (tpm170) REVERT: A 451 MET cc_start: 0.7261 (ttp) cc_final: 0.7009 (ttp) REVERT: B 71 GLN cc_start: 0.7566 (mm110) cc_final: 0.6872 (mm110) REVERT: B 85 PHE cc_start: 0.8031 (t80) cc_final: 0.7718 (t80) REVERT: B 164 PHE cc_start: 0.7051 (m-80) cc_final: 0.6790 (m-80) REVERT: B 357 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6912 (tt) REVERT: B 449 HIS cc_start: 0.7229 (m170) cc_final: 0.7005 (m170) REVERT: B 451 MET cc_start: 0.7152 (ttp) cc_final: 0.6807 (ttp) outliers start: 16 outliers final: 7 residues processed: 185 average time/residue: 0.2293 time to fit residues: 52.7618 Evaluate side-chains 176 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 72 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6442 Z= 0.189 Angle : 0.615 9.735 8792 Z= 0.309 Chirality : 0.043 0.232 1086 Planarity : 0.004 0.041 1074 Dihedral : 3.928 16.248 860 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.53 % Allowed : 20.44 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.31), residues: 802 helix: 1.15 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -0.34 (0.56), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 324 HIS 0.005 0.001 HIS A 57 PHE 0.017 0.001 PHE B 459 TYR 0.019 0.002 TYR B 313 ARG 0.006 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7937 (mp) REVERT: A 71 GLN cc_start: 0.7528 (mm110) cc_final: 0.7123 (mm110) REVERT: A 72 ARG cc_start: 0.7817 (tmt-80) cc_final: 0.7527 (tmt-80) REVERT: A 77 ARG cc_start: 0.8055 (mmt90) cc_final: 0.7846 (mmt90) REVERT: A 117 MET cc_start: 0.7044 (mmp) cc_final: 0.6689 (mmt) REVERT: A 332 LEU cc_start: 0.7810 (mm) cc_final: 0.7483 (mm) REVERT: A 357 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7111 (tt) REVERT: A 451 MET cc_start: 0.7244 (ttp) cc_final: 0.6991 (ttp) REVERT: A 452 GLN cc_start: 0.7690 (tp-100) cc_final: 0.7225 (tp-100) REVERT: B 44 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7839 (mp) REVERT: B 71 GLN cc_start: 0.7555 (mm110) cc_final: 0.6849 (mm110) REVERT: B 85 PHE cc_start: 0.8069 (t80) cc_final: 0.7726 (t80) REVERT: B 332 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7703 (mm) REVERT: B 357 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6981 (tt) REVERT: B 383 ILE cc_start: 0.7817 (mt) cc_final: 0.7544 (tt) REVERT: B 451 MET cc_start: 0.7158 (ttp) cc_final: 0.6819 (ttp) REVERT: B 452 GLN cc_start: 0.7575 (tp-100) cc_final: 0.7247 (tp-100) outliers start: 24 outliers final: 11 residues processed: 186 average time/residue: 0.2360 time to fit residues: 54.5278 Evaluate side-chains 187 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 77 optimal weight: 0.0060 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 64 optimal weight: 0.1980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6442 Z= 0.183 Angle : 0.616 9.372 8792 Z= 0.306 Chirality : 0.042 0.260 1086 Planarity : 0.004 0.040 1074 Dihedral : 3.842 16.155 860 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.85 % Allowed : 21.18 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.31), residues: 802 helix: 1.21 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -0.29 (0.56), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 92 HIS 0.011 0.001 HIS B 449 PHE 0.014 0.001 PHE A 420 TYR 0.019 0.002 TYR B 313 ARG 0.002 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 71 GLN cc_start: 0.7509 (mm110) cc_final: 0.7114 (mm110) REVERT: A 72 ARG cc_start: 0.7784 (tmt-80) cc_final: 0.6904 (tmt-80) REVERT: A 332 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7620 (mm) REVERT: A 357 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7327 (tp) REVERT: A 451 MET cc_start: 0.7253 (ttp) cc_final: 0.7040 (ttp) REVERT: B 71 GLN cc_start: 0.7550 (mm110) cc_final: 0.6852 (mm110) REVERT: B 114 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7575 (mp) REVERT: B 196 CYS cc_start: 0.4743 (OUTLIER) cc_final: 0.4483 (t) REVERT: B 332 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7714 (mm) REVERT: B 357 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.6866 (tt) REVERT: B 360 GLN cc_start: 0.6703 (tm-30) cc_final: 0.6315 (tm-30) REVERT: B 361 GLN cc_start: 0.7158 (mp10) cc_final: 0.6772 (mp10) REVERT: B 383 ILE cc_start: 0.7832 (mt) cc_final: 0.7557 (tt) REVERT: B 451 MET cc_start: 0.7170 (ttp) cc_final: 0.6838 (ttp) outliers start: 33 outliers final: 14 residues processed: 176 average time/residue: 0.2476 time to fit residues: 53.7160 Evaluate side-chains 188 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6442 Z= 0.249 Angle : 0.655 10.548 8792 Z= 0.327 Chirality : 0.043 0.266 1086 Planarity : 0.004 0.038 1074 Dihedral : 3.973 16.547 860 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.44 % Allowed : 22.50 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.31), residues: 802 helix: 1.05 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -0.22 (0.57), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 92 HIS 0.013 0.001 HIS B 449 PHE 0.017 0.001 PHE A 420 TYR 0.019 0.002 TYR B 313 ARG 0.005 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 179 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 71 GLN cc_start: 0.7533 (mm110) cc_final: 0.7145 (mm110) REVERT: A 72 ARG cc_start: 0.7794 (tmt-80) cc_final: 0.6782 (tmt-80) REVERT: A 266 ASP cc_start: 0.7781 (m-30) cc_final: 0.7496 (t0) REVERT: A 332 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7778 (mm) REVERT: A 361 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6498 (mt0) REVERT: A 387 SER cc_start: 0.8023 (t) cc_final: 0.7710 (t) REVERT: A 416 HIS cc_start: 0.7730 (t-90) cc_final: 0.7467 (t-90) REVERT: B 71 GLN cc_start: 0.7572 (mm110) cc_final: 0.6875 (mm110) REVERT: B 114 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7670 (mp) REVERT: B 196 CYS cc_start: 0.4827 (OUTLIER) cc_final: 0.4613 (t) REVERT: B 262 GLU cc_start: 0.7275 (tp30) cc_final: 0.6892 (tp30) REVERT: B 306 THR cc_start: 0.7918 (m) cc_final: 0.7699 (t) REVERT: B 310 PHE cc_start: 0.7890 (m-80) cc_final: 0.7603 (m-80) REVERT: B 332 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7795 (mm) REVERT: B 360 GLN cc_start: 0.6709 (tm-30) cc_final: 0.6361 (tm-30) REVERT: B 361 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6843 (mp10) REVERT: B 383 ILE cc_start: 0.7869 (mt) cc_final: 0.7569 (tt) REVERT: B 451 MET cc_start: 0.7213 (ttp) cc_final: 0.6889 (ttp) outliers start: 37 outliers final: 18 residues processed: 193 average time/residue: 0.2435 time to fit residues: 58.4997 Evaluate side-chains 197 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 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 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6442 Z= 0.244 Angle : 0.674 10.877 8792 Z= 0.331 Chirality : 0.044 0.294 1086 Planarity : 0.004 0.040 1074 Dihedral : 4.002 16.043 860 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.59 % Allowed : 24.41 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.31), residues: 802 helix: 0.93 (0.20), residues: 646 sheet: None (None), residues: 0 loop : 0.14 (0.62), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 92 HIS 0.014 0.002 HIS A 449 PHE 0.016 0.001 PHE A 420 TYR 0.019 0.002 TYR A 313 ARG 0.005 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7945 (mp) REVERT: A 71 GLN cc_start: 0.7560 (mm110) cc_final: 0.7156 (mm110) REVERT: A 72 ARG cc_start: 0.7798 (tmt-80) cc_final: 0.6796 (tmt-80) REVERT: A 266 ASP cc_start: 0.7770 (m-30) cc_final: 0.7499 (t0) REVERT: A 332 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7806 (mm) REVERT: A 361 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6422 (mt0) REVERT: A 387 SER cc_start: 0.8023 (t) cc_final: 0.7731 (t) REVERT: A 416 HIS cc_start: 0.7749 (t-90) cc_final: 0.7409 (t-90) REVERT: A 423 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7629 (tt) REVERT: B 71 GLN cc_start: 0.7579 (mm110) cc_final: 0.6875 (mm110) REVERT: B 85 PHE cc_start: 0.8111 (t80) cc_final: 0.7589 (t80) REVERT: B 114 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7611 (mp) REVERT: B 196 CYS cc_start: 0.4797 (OUTLIER) cc_final: 0.4570 (t) REVERT: B 262 GLU cc_start: 0.7257 (tp30) cc_final: 0.6983 (tp30) REVERT: B 332 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7767 (mm) REVERT: B 360 GLN cc_start: 0.6667 (tm-30) cc_final: 0.6363 (tm-30) REVERT: B 361 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6867 (mp10) REVERT: B 383 ILE cc_start: 0.7866 (mt) cc_final: 0.7557 (tt) REVERT: B 451 MET cc_start: 0.7199 (ttp) cc_final: 0.6895 (ttp) REVERT: B 462 LEU cc_start: 0.7836 (tt) cc_final: 0.7627 (tp) outliers start: 38 outliers final: 21 residues processed: 196 average time/residue: 0.2353 time to fit residues: 57.8632 Evaluate side-chains 212 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6442 Z= 0.241 Angle : 0.673 11.330 8792 Z= 0.329 Chirality : 0.044 0.316 1086 Planarity : 0.004 0.040 1074 Dihedral : 3.981 16.285 860 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.59 % Allowed : 24.85 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.31), residues: 802 helix: 0.92 (0.20), residues: 644 sheet: None (None), residues: 0 loop : 0.01 (0.61), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 92 HIS 0.014 0.002 HIS B 449 PHE 0.015 0.001 PHE A 420 TYR 0.020 0.002 TYR B 313 ARG 0.006 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7949 (mp) REVERT: A 71 GLN cc_start: 0.7550 (mm110) cc_final: 0.7162 (mm110) REVERT: A 72 ARG cc_start: 0.7793 (tmt-80) cc_final: 0.6762 (tmt-80) REVERT: A 266 ASP cc_start: 0.7762 (m-30) cc_final: 0.7465 (t0) REVERT: A 332 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7800 (mm) REVERT: A 361 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6502 (mt0) REVERT: A 362 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7952 (t) REVERT: A 387 SER cc_start: 0.8022 (t) cc_final: 0.7733 (t) REVERT: A 416 HIS cc_start: 0.7759 (t-90) cc_final: 0.7488 (t-170) REVERT: A 423 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7636 (tt) REVERT: B 71 GLN cc_start: 0.7580 (mm110) cc_final: 0.6872 (mm110) REVERT: B 85 PHE cc_start: 0.8146 (t80) cc_final: 0.7624 (t80) REVERT: B 114 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7605 (mp) REVERT: B 196 CYS cc_start: 0.4729 (OUTLIER) cc_final: 0.4511 (t) REVERT: B 262 GLU cc_start: 0.7296 (tp30) cc_final: 0.6862 (tp30) REVERT: B 332 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7746 (mm) REVERT: B 360 GLN cc_start: 0.6636 (tm-30) cc_final: 0.6378 (tm-30) REVERT: B 361 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6911 (mp10) REVERT: B 383 ILE cc_start: 0.7851 (mt) cc_final: 0.7529 (tt) REVERT: B 451 MET cc_start: 0.7201 (ttp) cc_final: 0.6894 (ttp) REVERT: B 462 LEU cc_start: 0.7841 (tt) cc_final: 0.7632 (tp) outliers start: 38 outliers final: 23 residues processed: 201 average time/residue: 0.2301 time to fit residues: 57.7385 Evaluate side-chains 213 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6442 Z= 0.219 Angle : 0.668 11.126 8792 Z= 0.325 Chirality : 0.043 0.330 1086 Planarity : 0.004 0.041 1074 Dihedral : 3.939 16.124 860 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.29 % Allowed : 26.91 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.31), residues: 802 helix: 0.93 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -0.02 (0.61), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 92 HIS 0.015 0.002 HIS B 449 PHE 0.014 0.001 PHE B 420 TYR 0.021 0.002 TYR B 313 ARG 0.003 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 71 GLN cc_start: 0.7531 (mm110) cc_final: 0.7131 (mm110) REVERT: A 72 ARG cc_start: 0.7795 (tmt-80) cc_final: 0.6750 (tmt-80) REVERT: A 266 ASP cc_start: 0.7742 (m-30) cc_final: 0.7453 (t0) REVERT: A 274 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8127 (p) REVERT: A 332 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7785 (mm) REVERT: A 362 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7925 (t) REVERT: A 387 SER cc_start: 0.8034 (t) cc_final: 0.7714 (t) REVERT: A 416 HIS cc_start: 0.7739 (t-90) cc_final: 0.7437 (t-170) REVERT: B 71 GLN cc_start: 0.7575 (mm110) cc_final: 0.6865 (mm110) REVERT: B 85 PHE cc_start: 0.8114 (t80) cc_final: 0.7549 (t80) REVERT: B 109 LEU cc_start: 0.7403 (mp) cc_final: 0.7196 (mp) REVERT: B 114 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7569 (mp) REVERT: B 196 CYS cc_start: 0.4761 (OUTLIER) cc_final: 0.4463 (t) REVERT: B 262 GLU cc_start: 0.7192 (tp30) cc_final: 0.6784 (tp30) REVERT: B 332 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7703 (mm) REVERT: B 360 GLN cc_start: 0.6589 (tm-30) cc_final: 0.6386 (tm-30) REVERT: B 361 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: B 383 ILE cc_start: 0.7832 (mt) cc_final: 0.7526 (tt) REVERT: B 451 MET cc_start: 0.7199 (ttp) cc_final: 0.6892 (ttp) outliers start: 36 outliers final: 24 residues processed: 206 average time/residue: 0.2147 time to fit residues: 55.4183 Evaluate side-chains 219 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 6442 Z= 0.322 Angle : 0.745 12.029 8792 Z= 0.368 Chirality : 0.047 0.341 1086 Planarity : 0.005 0.041 1074 Dihedral : 4.243 18.770 860 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 6.03 % Allowed : 26.76 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.31), residues: 802 helix: 0.71 (0.20), residues: 640 sheet: None (None), residues: 0 loop : 0.02 (0.61), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 92 HIS 0.019 0.002 HIS B 449 PHE 0.018 0.001 PHE A 420 TYR 0.024 0.002 TYR B 313 ARG 0.009 0.001 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7013 (tp-100) cc_final: 0.6661 (tp-100) REVERT: A 44 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7948 (mp) REVERT: A 71 GLN cc_start: 0.7597 (mm110) cc_final: 0.7203 (mm110) REVERT: A 72 ARG cc_start: 0.7821 (tmt-80) cc_final: 0.6796 (tmt-80) REVERT: A 77 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7768 (mtt90) REVERT: A 266 ASP cc_start: 0.7683 (m-30) cc_final: 0.7478 (t0) REVERT: A 274 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8177 (p) REVERT: A 332 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7854 (mm) REVERT: A 347 LEU cc_start: 0.8403 (mp) cc_final: 0.7975 (mm) REVERT: A 361 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6724 (mt0) REVERT: A 362 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7971 (t) REVERT: A 387 SER cc_start: 0.7999 (t) cc_final: 0.7692 (t) REVERT: A 416 HIS cc_start: 0.7866 (t-90) cc_final: 0.7526 (t-170) REVERT: B 71 GLN cc_start: 0.7608 (mm110) cc_final: 0.6901 (mm110) REVERT: B 85 PHE cc_start: 0.8144 (t80) cc_final: 0.7642 (t80) REVERT: B 196 CYS cc_start: 0.4881 (OUTLIER) cc_final: 0.4663 (t) REVERT: B 262 GLU cc_start: 0.7315 (tp30) cc_final: 0.6812 (tp30) REVERT: B 332 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7807 (mm) REVERT: B 360 GLN cc_start: 0.6707 (tm-30) cc_final: 0.6377 (tm-30) REVERT: B 361 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: B 383 ILE cc_start: 0.7900 (mt) cc_final: 0.7568 (tt) REVERT: B 451 MET cc_start: 0.7307 (ttp) cc_final: 0.7023 (ttp) outliers start: 41 outliers final: 26 residues processed: 214 average time/residue: 0.2242 time to fit residues: 59.8673 Evaluate side-chains 224 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 19 optimal weight: 0.0970 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6442 Z= 0.208 Angle : 0.701 11.566 8792 Z= 0.336 Chirality : 0.043 0.351 1086 Planarity : 0.005 0.042 1074 Dihedral : 4.050 17.855 860 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.00 % Allowed : 28.97 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.31), residues: 802 helix: 0.85 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -0.01 (0.60), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 92 HIS 0.016 0.002 HIS B 449 PHE 0.014 0.001 PHE B 420 TYR 0.023 0.002 TYR B 313 ARG 0.006 0.000 ARG A 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.6900 (tp-100) cc_final: 0.6664 (tp-100) REVERT: A 44 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7865 (mp) REVERT: A 47 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7531 (mm) REVERT: A 71 GLN cc_start: 0.7545 (mm110) cc_final: 0.7151 (mm110) REVERT: A 72 ARG cc_start: 0.7768 (tmt-80) cc_final: 0.6731 (tmt-80) REVERT: A 182 ARG cc_start: 0.8747 (mmp80) cc_final: 0.8408 (mmt-90) REVERT: A 266 ASP cc_start: 0.7673 (m-30) cc_final: 0.7388 (t0) REVERT: A 332 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7566 (mm) REVERT: A 347 LEU cc_start: 0.8316 (mp) cc_final: 0.7876 (mm) REVERT: A 361 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6459 (mt0) REVERT: A 362 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7922 (t) REVERT: A 387 SER cc_start: 0.7905 (t) cc_final: 0.7621 (t) REVERT: A 416 HIS cc_start: 0.7692 (t-90) cc_final: 0.7365 (t-170) REVERT: B 71 GLN cc_start: 0.7577 (mm110) cc_final: 0.6856 (mm110) REVERT: B 85 PHE cc_start: 0.8107 (t80) cc_final: 0.7537 (t80) REVERT: B 109 LEU cc_start: 0.7387 (mp) cc_final: 0.7169 (mp) REVERT: B 196 CYS cc_start: 0.4717 (OUTLIER) cc_final: 0.4415 (t) REVERT: B 332 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7512 (mm) REVERT: B 361 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6929 (mp10) REVERT: B 383 ILE cc_start: 0.7815 (mt) cc_final: 0.7506 (tt) REVERT: B 451 MET cc_start: 0.7243 (ttp) cc_final: 0.6938 (ttp) outliers start: 34 outliers final: 23 residues processed: 203 average time/residue: 0.2316 time to fit residues: 58.8681 Evaluate side-chains 215 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 0.0040 chunk 26 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.157019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.135626 restraints weight = 9751.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.140253 restraints weight = 4894.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.143327 restraints weight = 3008.642| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6442 Z= 0.226 Angle : 0.676 10.515 8792 Z= 0.332 Chirality : 0.043 0.182 1086 Planarity : 0.005 0.043 1074 Dihedral : 4.045 18.945 860 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.15 % Allowed : 27.94 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.31), residues: 802 helix: 0.92 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -0.00 (0.60), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 92 HIS 0.016 0.002 HIS B 449 PHE 0.017 0.001 PHE B 420 TYR 0.022 0.002 TYR B 313 ARG 0.006 0.001 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1809.00 seconds wall clock time: 34 minutes 16.41 seconds (2056.41 seconds total)