Starting phenix.real_space_refine on Fri Jul 19 20:02:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpf_18549/07_2024/8qpf_18549.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpf_18549/07_2024/8qpf_18549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpf_18549/07_2024/8qpf_18549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpf_18549/07_2024/8qpf_18549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpf_18549/07_2024/8qpf_18549.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpf_18549/07_2024/8qpf_18549.cif" } resolution = 2.53 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= 0.026 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 57 5.16 5 C 5850 2.51 5 N 1434 2.21 5 O 1744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C ASP 289": "OD1" <-> "OD2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9085 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2961 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 8, 'TRANS': 380} Chain breaks: 1 Chain: "B" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2961 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 8, 'TRANS': 380} Chain breaks: 1 Chain: "C" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2961 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 8, 'TRANS': 380} Chain breaks: 1 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Time building chain proxies: 5.18, per 1000 atoms: 0.57 Number of scatterers: 9085 At special positions: 0 Unit cell: (87.36, 94.08, 80.64, 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 57 16.00 O 1744 8.00 N 1434 7.00 C 5850 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 - 3.50 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: 3.89 Conformation dependent library (CDL) restraints added in 1.6 seconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 3 sheets defined 78.3% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 2 through 32 removed outlier: 3.511A pdb=" N ASN A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 59 removed outlier: 4.054A pdb=" N PHE A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 87 through 110 removed outlier: 4.010A pdb=" N GLY A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 129 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 203 through 226 removed outlier: 3.570A pdb=" N GLY A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 256 removed outlier: 3.557A pdb=" N VAL A 236 " --> pdb=" O MET A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 280 removed outlier: 3.750A pdb=" N PHE A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 311 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 323 through 338 removed outlier: 4.215A pdb=" N ALA A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 348 through 382 removed outlier: 3.532A pdb=" N PHE A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 370 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Proline residue: A 371 - end of helix removed outlier: 3.711A pdb=" N VAL A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 395 through 398 removed outlier: 3.931A pdb=" N GLY A 398 " --> pdb=" O LEU A 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 398' Processing helix chain 'B' and resid 3 through 32 removed outlier: 3.550A pdb=" N ASN B 32 " --> pdb=" O PHE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 59 removed outlier: 4.012A pdb=" N PHE B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 66 Processing helix chain 'B' and resid 87 through 108 removed outlier: 3.636A pdb=" N ALA B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 115 through 129 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 203 through 226 removed outlier: 3.558A pdb=" N GLY B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 256 removed outlier: 3.545A pdb=" N VAL B 236 " --> pdb=" O MET B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 280 removed outlier: 3.686A pdb=" N PHE B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 311 Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 323 through 338 removed outlier: 4.211A pdb=" N ALA B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 348 through 382 removed outlier: 3.533A pdb=" N PHE B 353 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B 370 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Proline residue: B 371 - end of helix removed outlier: 3.666A pdb=" N VAL B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 394 Processing helix chain 'B' and resid 395 through 398 removed outlier: 3.967A pdb=" N GLY B 398 " --> pdb=" O LEU B 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 395 through 398' Processing helix chain 'C' and resid 3 through 32 removed outlier: 3.547A pdb=" N ASN C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 59 removed outlier: 4.001A pdb=" N PHE C 49 " --> pdb=" O ASN C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 66 Processing helix chain 'C' and resid 87 through 110 removed outlier: 3.981A pdb=" N GLY C 108 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C 109 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 129 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 203 through 226 removed outlier: 3.505A pdb=" N GLY C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 256 removed outlier: 3.567A pdb=" N VAL C 236 " --> pdb=" O MET C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 280 removed outlier: 3.738A pdb=" N PHE C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 311 Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 323 through 338 removed outlier: 4.200A pdb=" N ALA C 335 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 343 Processing helix chain 'C' and resid 348 through 382 removed outlier: 3.516A pdb=" N PHE C 353 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 370 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Proline residue: C 371 - end of helix removed outlier: 3.628A pdb=" N VAL C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 394 Processing helix chain 'C' and resid 395 through 398 removed outlier: 3.975A pdb=" N GLY C 398 " --> pdb=" O LEU C 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 395 through 398' Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 191 removed outlier: 3.515A pdb=" N GLY B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 191 653 hydrogen bonds defined for protein. 1935 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: 2.77 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2735 1.35 - 1.47: 2435 1.47 - 1.59: 3851 1.59 - 1.71: 0 1.71 - 1.83: 78 Bond restraints: 9099 Sorted by residual: bond pdb=" CB TRP B 218 " pdb=" CG TRP B 218 " ideal model delta sigma weight residual 1.498 1.419 0.079 3.10e-02 1.04e+03 6.43e+00 bond pdb=" CB TRP A 218 " pdb=" CG TRP A 218 " ideal model delta sigma weight residual 1.498 1.421 0.077 3.10e-02 1.04e+03 6.17e+00 bond pdb=" CB TRP C 218 " pdb=" CG TRP C 218 " ideal model delta sigma weight residual 1.498 1.424 0.074 3.10e-02 1.04e+03 5.64e+00 bond pdb=" CG LEU B 216 " pdb=" CD2 LEU B 216 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.41e+00 bond pdb=" CG LEU A 216 " pdb=" CD2 LEU A 216 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.80e+00 ... (remaining 9094 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.18: 196 107.18 - 113.93: 5024 113.93 - 120.69: 4004 120.69 - 127.44: 3042 127.44 - 134.19: 106 Bond angle restraints: 12372 Sorted by residual: angle pdb=" CB MET A 97 " pdb=" CG MET A 97 " pdb=" SD MET A 97 " ideal model delta sigma weight residual 112.70 130.06 -17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" CB MET C 97 " pdb=" CG MET C 97 " pdb=" SD MET C 97 " ideal model delta sigma weight residual 112.70 127.04 -14.34 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C CYS B 255 " pdb=" N ILE B 256 " pdb=" CA ILE B 256 " ideal model delta sigma weight residual 121.97 129.84 -7.87 1.80e+00 3.09e-01 1.91e+01 angle pdb=" C CYS A 255 " pdb=" N ILE A 256 " pdb=" CA ILE A 256 " ideal model delta sigma weight residual 121.97 129.82 -7.85 1.80e+00 3.09e-01 1.90e+01 angle pdb=" C CYS C 255 " pdb=" N ILE C 256 " pdb=" CA ILE C 256 " ideal model delta sigma weight residual 121.97 129.80 -7.83 1.80e+00 3.09e-01 1.89e+01 ... (remaining 12367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4515 17.18 - 34.36: 453 34.36 - 51.54: 103 51.54 - 68.72: 20 68.72 - 85.90: 6 Dihedral angle restraints: 5097 sinusoidal: 1842 harmonic: 3255 Sorted by residual: dihedral pdb=" CA THR A 104 " pdb=" C THR A 104 " pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA THR C 104 " pdb=" C THR C 104 " pdb=" N ILE C 105 " pdb=" CA ILE C 105 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA THR B 104 " pdb=" C THR B 104 " pdb=" N ILE B 105 " pdb=" CA ILE B 105 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1269 0.072 - 0.144: 153 0.144 - 0.215: 15 0.215 - 0.287: 0 0.287 - 0.359: 3 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CB ILE C 256 " pdb=" CA ILE C 256 " pdb=" CG1 ILE C 256 " pdb=" CG2 ILE C 256 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE B 256 " pdb=" CA ILE B 256 " pdb=" CG1 ILE B 256 " pdb=" CG2 ILE B 256 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB ILE A 256 " pdb=" CA ILE A 256 " pdb=" CG1 ILE A 256 " pdb=" CG2 ILE A 256 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 1437 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 204 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO C 205 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 205 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 205 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 204 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 205 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 205 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 205 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO A 205 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.031 5.00e-02 4.00e+02 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2211 2.79 - 3.31: 8642 3.31 - 3.84: 17312 3.84 - 4.37: 20634 4.37 - 4.90: 34349 Nonbonded interactions: 83148 Sorted by model distance: nonbonded pdb=" OG SER A 234 " pdb=" OG SER B 90 " model vdw 2.257 2.440 nonbonded pdb=" O LEU B 204 " pdb=" OG1 THR B 207 " model vdw 2.289 2.440 nonbonded pdb=" O LEU A 204 " pdb=" OG1 THR A 207 " model vdw 2.311 2.440 nonbonded pdb=" NE1 TRP C 218 " pdb=" OG1 THR C 279 " model vdw 2.316 2.520 nonbonded pdb=" O PHE B 79 " pdb=" O HOH B 701 " model vdw 2.334 2.440 ... (remaining 83143 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' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.890 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9099 Z= 0.343 Angle : 0.838 17.365 12372 Z= 0.464 Chirality : 0.049 0.359 1440 Planarity : 0.007 0.072 1533 Dihedral : 14.754 85.903 3033 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.25 % Favored : 97.49 % Rotamer: Outliers : 0.75 % Allowed : 13.95 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1155 helix: 0.25 (0.16), residues: 837 sheet: None (None), residues: 0 loop : -1.69 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 218 HIS 0.005 0.001 HIS A 169 PHE 0.020 0.002 PHE B 221 TYR 0.026 0.003 TYR C 119 ARG 0.017 0.002 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 1.173 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 174 average time/residue: 1.2160 time to fit residues: 226.0339 Evaluate side-chains 123 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 231 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 95 GLN A 191 ASN A 197 ASN A 259 GLN B 22 GLN B 259 GLN C 197 ASN C 259 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9099 Z= 0.169 Angle : 0.515 8.660 12372 Z= 0.277 Chirality : 0.038 0.207 1440 Planarity : 0.004 0.040 1533 Dihedral : 4.574 24.528 1235 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.73 % Favored : 98.01 % Rotamer: Outliers : 2.24 % Allowed : 16.61 % Favored : 81.15 % 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: 1.42 (0.24), residues: 1155 helix: 1.74 (0.17), residues: 843 sheet: None (None), residues: 0 loop : -1.31 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 257 HIS 0.004 0.001 HIS C 323 PHE 0.018 0.001 PHE C 221 TYR 0.019 0.001 TYR A 119 ARG 0.005 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.016 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 145 average time/residue: 1.2177 time to fit residues: 189.0313 Evaluate side-chains 133 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 222 ASN B 22 GLN B 222 ASN B 323 HIS C 95 GLN C 222 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9099 Z= 0.174 Angle : 0.484 6.638 12372 Z= 0.263 Chirality : 0.037 0.149 1440 Planarity : 0.003 0.034 1533 Dihedral : 4.103 15.635 1227 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.99 % Favored : 97.75 % Rotamer: Outliers : 2.45 % Allowed : 17.15 % Favored : 80.40 % 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: 2.26 (0.25), residues: 1155 helix: 2.41 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -1.04 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 257 HIS 0.005 0.001 HIS B 323 PHE 0.014 0.001 PHE A 221 TYR 0.019 0.001 TYR B 119 ARG 0.003 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 0.964 Fit side-chains REVERT: B 312 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8588 (mttp) REVERT: B 399 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.5484 (pt0) outliers start: 23 outliers final: 13 residues processed: 143 average time/residue: 1.2075 time to fit residues: 184.8485 Evaluate side-chains 138 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 0.0970 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 197 ASN B 22 GLN B 222 ASN C 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9099 Z= 0.149 Angle : 0.485 7.306 12372 Z= 0.257 Chirality : 0.037 0.152 1440 Planarity : 0.003 0.031 1533 Dihedral : 4.009 15.191 1227 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.42 % Favored : 97.32 % Rotamer: Outliers : 2.56 % Allowed : 18.10 % Favored : 79.34 % 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: 2.49 (0.25), residues: 1155 helix: 2.73 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -1.20 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 257 HIS 0.002 0.001 HIS A 323 PHE 0.025 0.001 PHE B 221 TYR 0.015 0.001 TYR B 119 ARG 0.003 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 0.897 Fit side-chains REVERT: B 218 TRP cc_start: 0.8174 (OUTLIER) cc_final: 0.7880 (m-90) outliers start: 24 outliers final: 16 residues processed: 144 average time/residue: 1.1293 time to fit residues: 174.7544 Evaluate side-chains 140 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 197 ASN A 222 ASN A 258 GLN B 22 GLN C 45 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9099 Z= 0.249 Angle : 0.515 7.695 12372 Z= 0.276 Chirality : 0.038 0.143 1440 Planarity : 0.003 0.029 1533 Dihedral : 3.962 14.699 1227 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.08 % Favored : 97.66 % Rotamer: Outliers : 2.56 % Allowed : 18.00 % Favored : 79.45 % 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: 2.72 (0.25), residues: 1155 helix: 2.75 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 257 HIS 0.002 0.001 HIS C 169 PHE 0.026 0.001 PHE B 221 TYR 0.011 0.001 TYR A 119 ARG 0.003 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.005 Fit side-chains REVERT: B 218 TRP cc_start: 0.8283 (OUTLIER) cc_final: 0.7895 (m-90) REVERT: C 191 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.7083 (p0) outliers start: 24 outliers final: 14 residues processed: 140 average time/residue: 1.1553 time to fit residues: 173.7274 Evaluate side-chains 132 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN B 22 GLN B 191 ASN B 197 ASN C 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9099 Z= 0.279 Angle : 0.538 7.997 12372 Z= 0.288 Chirality : 0.039 0.138 1440 Planarity : 0.003 0.029 1533 Dihedral : 4.029 14.552 1227 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.16 % Favored : 97.58 % Rotamer: Outliers : 2.77 % Allowed : 18.00 % Favored : 79.23 % 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: 2.78 (0.25), residues: 1155 helix: 2.78 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -0.83 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 257 HIS 0.003 0.001 HIS B 169 PHE 0.027 0.001 PHE B 221 TYR 0.013 0.001 TYR C 119 ARG 0.003 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.002 Fit side-chains REVERT: B 218 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7947 (m-90) REVERT: B 312 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8680 (mttp) REVERT: C 218 TRP cc_start: 0.8145 (OUTLIER) cc_final: 0.7356 (t-100) outliers start: 26 outliers final: 17 residues processed: 141 average time/residue: 1.2584 time to fit residues: 189.8789 Evaluate side-chains 133 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 307 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 109 optimal weight: 0.0370 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 197 ASN A 222 ASN B 22 GLN B 197 ASN C 222 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9099 Z= 0.152 Angle : 0.506 8.746 12372 Z= 0.267 Chirality : 0.037 0.145 1440 Planarity : 0.003 0.030 1533 Dihedral : 3.996 15.411 1227 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.68 % Favored : 97.06 % Rotamer: Outliers : 2.56 % Allowed : 19.06 % Favored : 78.38 % 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: 2.84 (0.25), residues: 1155 helix: 2.97 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 218 HIS 0.003 0.001 HIS C 323 PHE 0.022 0.001 PHE B 221 TYR 0.014 0.001 TYR C 119 ARG 0.002 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.973 Fit side-chains REVERT: A 309 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7167 (mt-10) REVERT: B 218 TRP cc_start: 0.8219 (OUTLIER) cc_final: 0.7946 (m-90) REVERT: B 312 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8679 (mttp) outliers start: 24 outliers final: 17 residues processed: 141 average time/residue: 1.1234 time to fit residues: 170.1797 Evaluate side-chains 136 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 218 TRP Chi-restraints excluded: chain C residue 231 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 222 ASN B 22 GLN C 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9099 Z= 0.186 Angle : 0.524 10.536 12372 Z= 0.274 Chirality : 0.037 0.144 1440 Planarity : 0.003 0.029 1533 Dihedral : 3.924 15.258 1227 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.42 % Favored : 97.32 % Rotamer: Outliers : 2.13 % Allowed : 19.81 % Favored : 78.06 % 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: 2.84 (0.25), residues: 1155 helix: 2.96 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 218 HIS 0.003 0.001 HIS C 323 PHE 0.022 0.001 PHE B 221 TYR 0.014 0.001 TYR C 119 ARG 0.002 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.012 Fit side-chains REVERT: B 218 TRP cc_start: 0.8229 (OUTLIER) cc_final: 0.7958 (m-90) REVERT: B 312 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8696 (mttp) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 1.1941 time to fit residues: 172.8708 Evaluate side-chains 134 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 197 ASN A 222 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN C 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9099 Z= 0.153 Angle : 0.519 10.935 12372 Z= 0.272 Chirality : 0.037 0.149 1440 Planarity : 0.003 0.029 1533 Dihedral : 3.887 14.630 1227 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.68 % Favored : 97.06 % Rotamer: Outliers : 1.92 % Allowed : 20.13 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.90 (0.25), residues: 1155 helix: 3.00 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -0.96 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 218 HIS 0.003 0.001 HIS C 323 PHE 0.022 0.001 PHE B 221 TYR 0.024 0.001 TYR B 119 ARG 0.002 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.976 Fit side-chains REVERT: B 218 TRP cc_start: 0.8213 (OUTLIER) cc_final: 0.7943 (m-90) REVERT: B 312 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8684 (mttp) REVERT: B 341 GLN cc_start: 0.8658 (pp30) cc_final: 0.8305 (pt0) outliers start: 18 outliers final: 15 residues processed: 139 average time/residue: 1.1342 time to fit residues: 169.1387 Evaluate side-chains 137 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 222 ASN B 222 ASN C 191 ASN C 197 ASN C 222 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9099 Z= 0.188 Angle : 0.535 12.401 12372 Z= 0.278 Chirality : 0.038 0.148 1440 Planarity : 0.003 0.028 1533 Dihedral : 3.863 15.111 1227 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.16 % Favored : 97.58 % Rotamer: Outliers : 1.70 % Allowed : 20.45 % Favored : 77.85 % 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: 2.91 (0.25), residues: 1155 helix: 3.00 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -0.92 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 218 HIS 0.003 0.001 HIS C 323 PHE 0.021 0.001 PHE B 221 TYR 0.018 0.001 TYR C 119 ARG 0.002 0.000 ARG C 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.046 Fit side-chains REVERT: B 218 TRP cc_start: 0.8261 (OUTLIER) cc_final: 0.7997 (m-90) REVERT: B 312 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8687 (mttp) REVERT: B 341 GLN cc_start: 0.8638 (pp30) cc_final: 0.8209 (pp30) outliers start: 16 outliers final: 12 residues processed: 136 average time/residue: 1.1922 time to fit residues: 173.3775 Evaluate side-chains 136 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 218 TRP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 218 TRP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 218 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 9.9990 chunk 13 optimal weight: 0.0470 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 197 ASN A 198 GLN A 222 ASN B 22 GLN C 222 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.090620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.071833 restraints weight = 16544.565| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.00 r_work: 0.2635 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9099 Z= 0.171 Angle : 0.525 12.486 12372 Z= 0.274 Chirality : 0.038 0.147 1440 Planarity : 0.003 0.028 1533 Dihedral : 3.879 14.439 1227 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.77 % Favored : 96.97 % Rotamer: Outliers : 1.92 % Allowed : 20.77 % Favored : 77.32 % 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: 2.94 (0.25), residues: 1155 helix: 3.02 (0.17), residues: 816 sheet: None (None), residues: 0 loop : -0.90 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 218 HIS 0.003 0.001 HIS C 323 PHE 0.022 0.001 PHE B 221 TYR 0.029 0.001 TYR B 119 ARG 0.002 0.000 ARG B 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3248.97 seconds wall clock time: 57 minutes 29.62 seconds (3449.62 seconds total)