Starting phenix.real_space_refine on Mon Mar 11 05:03:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/03_2024/8iq6_35658_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/03_2024/8iq6_35658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/03_2024/8iq6_35658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/03_2024/8iq6_35658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/03_2024/8iq6_35658_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/03_2024/8iq6_35658_updated.pdb" } resolution = 3.4 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= 0.000 sd= 0.066 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 52 5.16 5 C 4541 2.51 5 N 1203 2.21 5 O 1263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7059 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1560 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2342 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 238 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 845 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2046 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'7WT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.33, per 1000 atoms: 0.61 Number of scatterers: 7059 At special positions: 0 Unit cell: (71.3635, 97.7131, 125.161, 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 52 16.00 O 1263 8.00 N 1203 7.00 C 4541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 10 sheets defined 37.4% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.943A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 337 through 351 removed outlier: 3.782A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 16 through 24 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.706A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'R' and resid 30 through 61 removed outlier: 4.784A pdb=" N GLN R 60 " --> pdb=" O GLN R 56 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 93 Processing helix chain 'R' and resid 106 through 138 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 148 through 172 removed outlier: 3.894A pdb=" N VAL R 152 " --> pdb=" O THR R 148 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 196 through 228 Processing helix chain 'R' and resid 244 through 274 Proline residue: R 264 - end of helix Processing helix chain 'R' and resid 283 through 304 removed outlier: 4.429A pdb=" N MET R 292 " --> pdb=" O PHE R 288 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 312 No H-bonds generated for 'chain 'R' and resid 309 through 312' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.116A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.993A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.071A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.875A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.964A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.975A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.395A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.926A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.893A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1050 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: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1760 1.33 - 1.45: 1435 1.45 - 1.57: 3934 1.57 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 7200 Sorted by residual: bond pdb=" C02 7WT R 401 " pdb=" O01 7WT R 401 " ideal model delta sigma weight residual 1.414 1.538 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CA ALA R 293 " pdb=" CB ALA R 293 " ideal model delta sigma weight residual 1.532 1.477 0.055 1.62e-02 3.81e+03 1.14e+01 bond pdb=" C20 7WT R 401 " pdb=" C21 7WT R 401 " ideal model delta sigma weight residual 1.497 1.556 -0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" CA ALA R 289 " pdb=" CB ALA R 289 " ideal model delta sigma weight residual 1.530 1.482 0.049 1.69e-02 3.50e+03 8.30e+00 bond pdb=" C22 7WT R 401 " pdb=" C23 7WT R 401 " ideal model delta sigma weight residual 1.496 1.550 -0.054 2.00e-02 2.50e+03 7.20e+00 ... (remaining 7195 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.01: 73 105.01 - 112.26: 3764 112.26 - 119.51: 2201 119.51 - 126.76: 3664 126.76 - 134.01: 96 Bond angle restraints: 9798 Sorted by residual: angle pdb=" N LEU R 290 " pdb=" CA LEU R 290 " pdb=" C LEU R 290 " ideal model delta sigma weight residual 111.36 102.64 8.72 1.09e+00 8.42e-01 6.40e+01 angle pdb=" N MET R 292 " pdb=" CA MET R 292 " pdb=" C MET R 292 " ideal model delta sigma weight residual 113.38 107.19 6.19 1.23e+00 6.61e-01 2.53e+01 angle pdb=" N ALA R 293 " pdb=" CA ALA R 293 " pdb=" C ALA R 293 " ideal model delta sigma weight residual 112.04 105.37 6.67 1.44e+00 4.82e-01 2.15e+01 angle pdb=" C20 7WT R 401 " pdb=" C21 7WT R 401 " pdb=" C22 7WT R 401 " ideal model delta sigma weight residual 128.03 114.32 13.71 3.00e+00 1.11e-01 2.09e+01 angle pdb=" N LEU R 287 " pdb=" CA LEU R 287 " pdb=" C LEU R 287 " ideal model delta sigma weight residual 111.36 107.22 4.14 1.09e+00 8.42e-01 1.45e+01 ... (remaining 9793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 3607 15.89 - 31.77: 435 31.77 - 47.66: 134 47.66 - 63.55: 21 63.55 - 79.44: 7 Dihedral angle restraints: 4204 sinusoidal: 1438 harmonic: 2766 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -142.92 56.92 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA ARG R 100 " pdb=" C ARG R 100 " pdb=" N PHE R 101 " pdb=" CA PHE R 101 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA CYS N 99 " pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " ideal model delta sinusoidal sigma weight residual 79.00 13.87 65.13 1 2.00e+01 2.50e-03 1.39e+01 ... (remaining 4201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1079 0.078 - 0.156: 86 0.156 - 0.234: 2 0.234 - 0.312: 1 0.312 - 0.391: 2 Chirality restraints: 1170 Sorted by residual: chirality pdb=" C03 7WT R 401 " pdb=" C02 7WT R 401 " pdb=" C04 7WT R 401 " pdb=" C20 7WT R 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.92 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" C04 7WT R 401 " pdb=" C03 7WT R 401 " pdb=" C05 7WT R 401 " pdb=" C08 7WT R 401 " both_signs ideal model delta sigma weight residual False 2.63 2.97 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA LEU R 290 " pdb=" N LEU R 290 " pdb=" C LEU R 290 " pdb=" CB LEU R 290 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1167 not shown) Planarity restraints: 1222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C THR B 87 " -0.033 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO G 49 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 ... (remaining 1219 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1631 2.78 - 3.31: 6386 3.31 - 3.84: 11583 3.84 - 4.37: 12980 4.37 - 4.90: 23810 Nonbonded interactions: 56390 Sorted by model distance: nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.259 2.440 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.261 2.520 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.267 2.440 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.271 2.520 ... (remaining 56385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.760 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: 3.870 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.510 Find NCS groups from input model: 0.180 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.004 0.124 7200 Z= 0.252 Angle : 0.586 13.711 9798 Z= 0.324 Chirality : 0.045 0.391 1170 Planarity : 0.004 0.064 1222 Dihedral : 15.453 79.436 2401 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.29 % Allowed : 18.83 % Favored : 80.88 % 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: 1.39 (0.28), residues: 930 helix: 3.05 (0.27), residues: 354 sheet: 0.50 (0.36), residues: 202 loop : -1.01 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: R 217 LEU cc_start: 0.8668 (tp) cc_final: 0.8225 (tp) REVERT: R 291 ARG cc_start: 0.8164 (ptp-170) cc_final: 0.6998 (ptm160) outliers start: 2 outliers final: 1 residues processed: 119 average time/residue: 0.2197 time to fit residues: 33.8760 Evaluate side-chains 115 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7200 Z= 0.148 Angle : 0.428 5.983 9798 Z= 0.233 Chirality : 0.039 0.136 1170 Planarity : 0.003 0.037 1222 Dihedral : 5.034 54.181 1048 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.36 % Allowed : 17.08 % Favored : 79.56 % 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: 1.42 (0.28), residues: 930 helix: 3.03 (0.27), residues: 360 sheet: 0.55 (0.36), residues: 202 loop : -1.04 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE R 101 TYR 0.009 0.001 TYR N 95 ARG 0.005 0.000 ARG R 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: B 237 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8449 (p0) REVERT: R 59 ARG cc_start: 0.7847 (tmm-80) cc_final: 0.7268 (ttp-170) REVERT: R 115 MET cc_start: 0.8664 (mmm) cc_final: 0.8220 (tpt) REVERT: R 246 GLU cc_start: 0.7609 (mp0) cc_final: 0.7213 (tp30) outliers start: 23 outliers final: 14 residues processed: 129 average time/residue: 0.2015 time to fit residues: 34.3086 Evaluate side-chains 126 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 84 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7200 Z= 0.181 Angle : 0.429 5.154 9798 Z= 0.235 Chirality : 0.040 0.139 1170 Planarity : 0.003 0.040 1222 Dihedral : 4.824 50.562 1048 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.65 % Allowed : 16.93 % Favored : 79.42 % 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: 1.51 (0.28), residues: 930 helix: 3.21 (0.27), residues: 354 sheet: 0.49 (0.36), residues: 203 loop : -0.95 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.005 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: B 237 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8436 (p0) REVERT: R 59 ARG cc_start: 0.7844 (tmm-80) cc_final: 0.7366 (ttp-170) REVERT: R 115 MET cc_start: 0.8685 (mmm) cc_final: 0.8234 (tpt) REVERT: R 246 GLU cc_start: 0.7625 (mp0) cc_final: 0.7233 (tp30) outliers start: 25 outliers final: 14 residues processed: 131 average time/residue: 0.1931 time to fit residues: 33.6573 Evaluate side-chains 127 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 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 271 ASN R 243 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7200 Z= 0.173 Angle : 0.426 5.082 9798 Z= 0.233 Chirality : 0.040 0.138 1170 Planarity : 0.003 0.040 1222 Dihedral : 4.655 46.883 1048 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.77 % Allowed : 17.37 % Favored : 79.85 % 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: 1.54 (0.28), residues: 930 helix: 3.23 (0.27), residues: 354 sheet: 0.52 (0.36), residues: 203 loop : -0.95 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.005 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 292 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8670 (m-40) REVERT: B 237 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8410 (p0) REVERT: R 59 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7386 (ttp-170) REVERT: R 115 MET cc_start: 0.8739 (mmm) cc_final: 0.8282 (tpt) REVERT: R 200 PHE cc_start: 0.8423 (t80) cc_final: 0.8097 (t80) REVERT: R 246 GLU cc_start: 0.7596 (mp0) cc_final: 0.7218 (tp30) outliers start: 19 outliers final: 14 residues processed: 128 average time/residue: 0.1991 time to fit residues: 33.7864 Evaluate side-chains 131 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7200 Z= 0.296 Angle : 0.488 5.234 9798 Z= 0.265 Chirality : 0.041 0.142 1170 Planarity : 0.003 0.048 1222 Dihedral : 4.579 31.965 1046 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.36 % Allowed : 17.66 % Favored : 78.98 % 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: 1.35 (0.28), residues: 930 helix: 2.97 (0.27), residues: 361 sheet: 0.35 (0.36), residues: 199 loop : -0.95 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS R 81 PHE 0.017 0.001 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.004 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: B 237 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8516 (p0) REVERT: R 59 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7483 (ttp-170) REVERT: R 115 MET cc_start: 0.8816 (mmm) cc_final: 0.8349 (tpt) REVERT: R 200 PHE cc_start: 0.8535 (t80) cc_final: 0.8242 (t80) REVERT: R 246 GLU cc_start: 0.7580 (mp0) cc_final: 0.7243 (tp30) outliers start: 23 outliers final: 17 residues processed: 128 average time/residue: 0.2234 time to fit residues: 37.7982 Evaluate side-chains 128 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 296 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7200 Z= 0.192 Angle : 0.445 4.973 9798 Z= 0.243 Chirality : 0.040 0.139 1170 Planarity : 0.003 0.045 1222 Dihedral : 4.374 29.414 1046 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.77 % Allowed : 18.83 % Favored : 78.39 % 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 (0.29), residues: 930 helix: 3.04 (0.27), residues: 360 sheet: 0.45 (0.36), residues: 199 loop : -0.97 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.006 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 272 ASP cc_start: 0.8371 (m-30) cc_final: 0.8141 (m-30) REVERT: A 292 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8656 (m-40) REVERT: B 237 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8580 (p0) REVERT: R 59 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7471 (ttp-170) REVERT: R 200 PHE cc_start: 0.8525 (t80) cc_final: 0.8178 (t80) REVERT: R 246 GLU cc_start: 0.7516 (mp0) cc_final: 0.7218 (tp30) outliers start: 19 outliers final: 16 residues processed: 126 average time/residue: 0.2068 time to fit residues: 34.2371 Evaluate side-chains 129 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7200 Z= 0.181 Angle : 0.438 4.920 9798 Z= 0.239 Chirality : 0.040 0.137 1170 Planarity : 0.003 0.044 1222 Dihedral : 4.234 27.182 1046 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.92 % Allowed : 19.71 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.47 (0.29), residues: 930 helix: 3.07 (0.27), residues: 361 sheet: 0.55 (0.37), residues: 197 loop : -0.98 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.007 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 292 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8637 (m-40) REVERT: B 237 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8516 (p0) REVERT: R 59 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7473 (ttp-170) REVERT: R 200 PHE cc_start: 0.8459 (t80) cc_final: 0.8104 (t80) REVERT: R 217 LEU cc_start: 0.8639 (tp) cc_final: 0.8167 (tp) REVERT: R 246 GLU cc_start: 0.7488 (mp0) cc_final: 0.7197 (tp30) outliers start: 20 outliers final: 16 residues processed: 127 average time/residue: 0.2036 time to fit residues: 34.1895 Evaluate side-chains 130 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7200 Z= 0.189 Angle : 0.444 4.953 9798 Z= 0.242 Chirality : 0.040 0.137 1170 Planarity : 0.003 0.044 1222 Dihedral : 4.196 25.732 1046 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.65 % Allowed : 19.27 % Favored : 77.08 % 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: 1.46 (0.29), residues: 930 helix: 3.07 (0.27), residues: 361 sheet: 0.54 (0.37), residues: 197 loop : -0.99 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.007 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 292 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8641 (m-40) REVERT: B 237 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8518 (p0) REVERT: R 59 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7472 (ttp-170) REVERT: R 200 PHE cc_start: 0.8474 (t80) cc_final: 0.7972 (t80) REVERT: R 217 LEU cc_start: 0.8640 (tp) cc_final: 0.8173 (tp) REVERT: R 246 GLU cc_start: 0.7472 (mp0) cc_final: 0.7187 (tp30) outliers start: 25 outliers final: 19 residues processed: 130 average time/residue: 0.1957 time to fit residues: 33.6134 Evaluate side-chains 132 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.0570 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7200 Z= 0.168 Angle : 0.438 4.970 9798 Z= 0.238 Chirality : 0.040 0.137 1170 Planarity : 0.003 0.042 1222 Dihedral : 4.096 24.680 1046 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.36 % Allowed : 19.71 % Favored : 76.93 % 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: 1.50 (0.29), residues: 930 helix: 3.10 (0.27), residues: 361 sheet: 0.59 (0.37), residues: 197 loop : -0.98 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 292 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8636 (m-40) REVERT: B 237 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8452 (p0) REVERT: R 59 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7470 (ttp-170) REVERT: R 200 PHE cc_start: 0.8456 (t80) cc_final: 0.7946 (t80) REVERT: R 217 LEU cc_start: 0.8643 (tp) cc_final: 0.8190 (tp) REVERT: R 246 GLU cc_start: 0.7468 (mp0) cc_final: 0.7212 (tp30) outliers start: 23 outliers final: 19 residues processed: 128 average time/residue: 0.1963 time to fit residues: 33.3954 Evaluate side-chains 132 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7200 Z= 0.186 Angle : 0.445 5.315 9798 Z= 0.241 Chirality : 0.040 0.135 1170 Planarity : 0.003 0.043 1222 Dihedral : 4.110 25.417 1046 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.36 % Allowed : 19.56 % Favored : 77.08 % 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: 1.48 (0.29), residues: 930 helix: 3.08 (0.27), residues: 361 sheet: 0.56 (0.37), residues: 197 loop : -0.99 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG R 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 292 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8651 (m-40) REVERT: B 237 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8479 (p0) REVERT: R 59 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7464 (ttp-170) REVERT: R 200 PHE cc_start: 0.8476 (t80) cc_final: 0.7950 (t80) REVERT: R 217 LEU cc_start: 0.8637 (tp) cc_final: 0.8163 (tp) outliers start: 23 outliers final: 20 residues processed: 127 average time/residue: 0.1982 time to fit residues: 33.3198 Evaluate side-chains 135 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114498 restraints weight = 9478.643| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.50 r_work: 0.3011 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7200 Z= 0.179 Angle : 0.443 5.950 9798 Z= 0.239 Chirality : 0.040 0.138 1170 Planarity : 0.003 0.042 1222 Dihedral : 4.059 24.715 1046 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.21 % Allowed : 19.85 % Favored : 76.93 % 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: 1.51 (0.29), residues: 930 helix: 3.11 (0.27), residues: 361 sheet: 0.59 (0.37), residues: 197 loop : -0.97 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG R 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.20 seconds wall clock time: 31 minutes 42.16 seconds (1902.16 seconds total)