Starting phenix.real_space_refine on Tue Sep 24 19:26:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuq_43536/09_2024/8vuq_43536.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuq_43536/09_2024/8vuq_43536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuq_43536/09_2024/8vuq_43536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuq_43536/09_2024/8vuq_43536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuq_43536/09_2024/8vuq_43536.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuq_43536/09_2024/8vuq_43536.cif" } resolution = 3.85 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= 0.015 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 36 5.16 5 C 5500 2.51 5 N 1492 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8657 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2789 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2697 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 15, 'TRANS': 347} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 125 Chain: "G" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1617 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 209} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1554 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.81, per 1000 atoms: 0.79 Number of scatterers: 8657 At special positions: 0 Unit cell: (107, 113.848, 124.976, 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 36 16.00 O 1629 8.00 N 1492 7.00 C 5500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 149 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 91 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 19 sheets defined 24.9% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.570A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.937A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.554A pdb=" N PHE A 102 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 103 " --> pdb=" O ASP A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.506A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.797A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.518A pdb=" N GLN A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.659A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.502A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.757A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.832A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 107 through 119 removed outlier: 4.095A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.613A pdb=" N SER B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 133' Processing helix chain 'B' and resid 150 through 166 Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.933A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 removed outlier: 4.312A pdb=" N GLN B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.675A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.672A pdb=" N ARG B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.872A pdb=" N VAL B 339 " --> pdb=" O PRO B 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 196 through 198 No H-bonds generated for 'chain 'G' and resid 196 through 198' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.768A pdb=" N ASN I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 removed outlier: 3.751A pdb=" N ALA I 127 " --> pdb=" O GLU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 removed outlier: 3.749A pdb=" N HIS I 188 " --> pdb=" O GLN I 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 removed outlier: 3.502A pdb=" N LEU A 33 " --> pdb=" O VAL A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 6.734A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.731A pdb=" N VAL A 167 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 197 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 340 through 341 removed outlier: 3.734A pdb=" N ASN A 341 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 344 " --> pdb=" O ASN A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 367 Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 72 removed outlier: 7.047A pdb=" N ALA B 37 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 200 removed outlier: 3.878A pdb=" N PHE B 170 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP B 255 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL B 279 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 364 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 341 through 342 removed outlier: 3.572A pdb=" N VAL B 341 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 348 " --> pdb=" O VAL B 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.857A pdb=" N LEU G 81 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 60 removed outlier: 3.551A pdb=" N GLY G 59 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA G 97 " --> pdb=" O HIS G 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 129 through 133 removed outlier: 4.285A pdb=" N GLY G 148 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 193 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 147 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR G 185 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL G 190 " --> pdb=" O HIS G 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 129 through 133 removed outlier: 4.285A pdb=" N GLY G 148 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 193 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 147 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR G 185 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER G 186 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 159 through 163 Processing sheet with id=AB6, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.762A pdb=" N VAL I 10 " --> pdb=" O THR I 104 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP I 88 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN I 39 " --> pdb=" O ASP I 88 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR I 90 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL I 48 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 18 through 20 removed outlier: 4.072A pdb=" N VAL I 18 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE I 78 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER I 66 " --> pdb=" O SER I 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 114 through 118 removed outlier: 6.057A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 114 through 118 removed outlier: 6.057A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA I 173 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 154 through 155 removed outlier: 4.065A pdb=" N TRP I 148 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS I 149 " --> pdb=" O SER I 192 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER I 192 " --> pdb=" O LYS I 149 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 768 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: 2.41 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2801 1.34 - 1.46: 2083 1.46 - 1.58: 3917 1.58 - 1.70: 2 1.70 - 1.82: 60 Bond restraints: 8863 Sorted by residual: bond pdb=" CB PRO G 156 " pdb=" CG PRO G 156 " ideal model delta sigma weight residual 1.506 1.587 -0.081 3.90e-02 6.57e+02 4.28e+00 bond pdb=" N PRO G 156 " pdb=" CA PRO G 156 " ideal model delta sigma weight residual 1.468 1.435 0.033 1.70e-02 3.46e+03 3.80e+00 bond pdb=" CG PRO G 156 " pdb=" CD PRO G 156 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.18e+00 bond pdb=" CB PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.93e+00 bond pdb=" CA ASN I 53 " pdb=" CB ASN I 53 " ideal model delta sigma weight residual 1.539 1.598 -0.058 4.88e-02 4.20e+02 1.43e+00 ... (remaining 8858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 12010 2.82 - 5.64: 74 5.64 - 8.47: 8 8.47 - 11.29: 1 11.29 - 14.11: 1 Bond angle restraints: 12094 Sorted by residual: angle pdb=" CA PRO G 156 " pdb=" N PRO G 156 " pdb=" CD PRO G 156 " ideal model delta sigma weight residual 111.50 97.39 14.11 1.40e+00 5.10e-01 1.02e+02 angle pdb=" C THR I 83 " pdb=" CA THR I 83 " pdb=" CB THR I 83 " ideal model delta sigma weight residual 116.54 110.04 6.50 1.15e+00 7.56e-01 3.19e+01 angle pdb=" N PRO G 156 " pdb=" CD PRO G 156 " pdb=" CG PRO G 156 " ideal model delta sigma weight residual 103.80 98.76 5.04 1.20e+00 6.94e-01 1.76e+01 angle pdb=" CA THR I 83 " pdb=" C THR I 83 " pdb=" N GLU I 84 " ideal model delta sigma weight residual 119.52 116.77 2.75 7.90e-01 1.60e+00 1.21e+01 angle pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 112.00 107.37 4.63 1.40e+00 5.10e-01 1.09e+01 ... (remaining 12089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4498 17.96 - 35.91: 566 35.91 - 53.87: 147 53.87 - 71.82: 24 71.82 - 89.78: 12 Dihedral angle restraints: 5247 sinusoidal: 1891 harmonic: 3356 Sorted by residual: dihedral pdb=" CA ASP A 169 " pdb=" C ASP A 169 " pdb=" N ASP A 170 " pdb=" CA ASP A 170 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PRO A 142 " pdb=" C PRO A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta harmonic sigma weight residual -180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP I 138 " pdb=" CB ASP I 138 " pdb=" CG ASP I 138 " pdb=" OD1 ASP I 138 " ideal model delta sinusoidal sigma weight residual -30.00 -88.25 58.25 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 802 0.029 - 0.058: 393 0.058 - 0.087: 105 0.087 - 0.117: 82 0.117 - 0.146: 15 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CB THR G 91 " pdb=" CA THR G 91 " pdb=" OG1 THR G 91 " pdb=" CG2 THR G 91 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE B 227 " pdb=" N ILE B 227 " pdb=" C ILE B 227 " pdb=" CB ILE B 227 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA VAL G 40 " pdb=" N VAL G 40 " pdb=" C VAL G 40 " pdb=" CB VAL G 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 1394 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 155 " -0.089 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO G 156 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO G 156 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO G 156 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 303 " -0.045 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 304 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 318 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 319 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " -0.026 5.00e-02 4.00e+02 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 245 2.69 - 3.24: 8282 3.24 - 3.79: 12495 3.79 - 4.35: 15199 4.35 - 4.90: 26229 Nonbonded interactions: 62450 Sorted by model distance: nonbonded pdb=" O ASN I 53 " pdb=" ND2 ASN I 53 " model vdw 2.133 3.120 nonbonded pdb=" O MET I 3 " pdb=" OG SER I 25 " model vdw 2.146 3.040 nonbonded pdb=" O PHE B 195 " pdb=" N GLY B 197 " model vdw 2.163 3.120 nonbonded pdb=" OG SER A 93 " pdb=" OE2 GLU A 277 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN B 154 " pdb=" OG SER B 259 " model vdw 2.216 3.040 ... (remaining 62445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.610 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.450 Find NCS groups from input model: 0.120 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8863 Z= 0.184 Angle : 0.616 14.112 12094 Z= 0.328 Chirality : 0.042 0.146 1397 Planarity : 0.005 0.124 1541 Dihedral : 17.334 89.781 3071 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.06 % Favored : 87.51 % Rotamer: Outliers : 0.66 % Allowed : 35.83 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.68 (0.26), residues: 1153 helix: 0.75 (0.37), residues: 218 sheet: -1.03 (0.32), residues: 317 loop : -1.89 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 284 HIS 0.005 0.001 HIS B 332 PHE 0.009 0.001 PHE B 210 TYR 0.021 0.001 TYR B 321 ARG 0.004 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.023 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 132 average time/residue: 0.2051 time to fit residues: 37.1340 Evaluate side-chains 127 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 338 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.0270 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8863 Z= 0.180 Angle : 0.591 7.916 12094 Z= 0.309 Chirality : 0.043 0.138 1397 Planarity : 0.004 0.077 1541 Dihedral : 4.134 22.203 1244 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.62 % Favored : 87.94 % Rotamer: Outliers : 5.73 % Allowed : 29.00 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.58 (0.26), residues: 1153 helix: 0.88 (0.35), residues: 246 sheet: -0.80 (0.32), residues: 316 loop : -2.09 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.003 0.001 HIS B 332 PHE 0.012 0.001 PHE B 210 TYR 0.012 0.001 TYR B 321 ARG 0.003 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8089 (ptm160) REVERT: A 162 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6891 (m90) REVERT: A 295 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8937 (tp) REVERT: G 49 SER cc_start: 0.8747 (p) cc_final: 0.8390 (m) REVERT: G 180 GLN cc_start: 0.6071 (pm20) cc_final: 0.3725 (tm-30) REVERT: I 53 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7960 (p0) outliers start: 52 outliers final: 29 residues processed: 174 average time/residue: 0.1780 time to fit residues: 43.6438 Evaluate side-chains 155 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 30.0000 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8863 Z= 0.265 Angle : 0.610 7.696 12094 Z= 0.317 Chirality : 0.044 0.155 1397 Planarity : 0.004 0.066 1541 Dihedral : 4.294 23.027 1241 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.10 % Favored : 86.47 % Rotamer: Outliers : 6.95 % Allowed : 28.56 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.71 (0.26), residues: 1153 helix: 0.65 (0.34), residues: 253 sheet: -0.92 (0.32), residues: 320 loop : -2.12 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 160 HIS 0.003 0.001 HIS B 119 PHE 0.017 0.001 PHE A 152 TYR 0.014 0.001 TYR B 321 ARG 0.003 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 129 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8101 (ptm160) REVERT: B 206 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7904 (pp) REVERT: B 207 ASP cc_start: 0.8368 (p0) cc_final: 0.8038 (p0) REVERT: B 348 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8816 (pp) REVERT: B 378 TRP cc_start: 0.8481 (OUTLIER) cc_final: 0.7910 (t60) REVERT: G 49 SER cc_start: 0.8881 (p) cc_final: 0.8477 (m) outliers start: 63 outliers final: 42 residues processed: 176 average time/residue: 0.2028 time to fit residues: 50.1660 Evaluate side-chains 170 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 124 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 136 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 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 162 HIS ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8863 Z= 0.178 Angle : 0.579 7.800 12094 Z= 0.295 Chirality : 0.043 0.141 1397 Planarity : 0.004 0.059 1541 Dihedral : 4.201 22.284 1241 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.62 % Favored : 87.94 % Rotamer: Outliers : 6.06 % Allowed : 30.32 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.61 (0.26), residues: 1153 helix: 0.79 (0.34), residues: 250 sheet: -0.98 (0.31), residues: 319 loop : -2.00 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 148 HIS 0.005 0.001 HIS A 293 PHE 0.014 0.001 PHE A 152 TYR 0.023 0.001 TYR B 180 ARG 0.003 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 130 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8126 (ptm160) REVERT: B 206 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7857 (pp) REVERT: B 207 ASP cc_start: 0.8410 (p0) cc_final: 0.8101 (p0) REVERT: B 348 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8814 (pp) REVERT: B 378 TRP cc_start: 0.8470 (OUTLIER) cc_final: 0.7807 (t60) REVERT: G 49 SER cc_start: 0.8876 (p) cc_final: 0.8511 (m) REVERT: I 53 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7952 (p0) outliers start: 55 outliers final: 44 residues processed: 171 average time/residue: 0.2058 time to fit residues: 48.7586 Evaluate side-chains 174 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 125 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8863 Z= 0.350 Angle : 0.644 7.551 12094 Z= 0.335 Chirality : 0.045 0.148 1397 Planarity : 0.005 0.055 1541 Dihedral : 4.568 26.992 1241 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.88 % Favored : 85.69 % Rotamer: Outliers : 8.16 % Allowed : 28.56 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.81 (0.25), residues: 1153 helix: 0.53 (0.33), residues: 250 sheet: -1.04 (0.31), residues: 319 loop : -2.11 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 148 HIS 0.005 0.001 HIS A 293 PHE 0.015 0.002 PHE A 152 TYR 0.013 0.002 TYR G 95 ARG 0.005 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 123 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8099 (ptm160) REVERT: B 206 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7961 (pp) REVERT: B 207 ASP cc_start: 0.8496 (p0) cc_final: 0.8188 (p0) REVERT: B 348 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8747 (pp) REVERT: B 378 TRP cc_start: 0.8656 (OUTLIER) cc_final: 0.8057 (t60) REVERT: I 24 ARG cc_start: 0.8805 (ttt90) cc_final: 0.8574 (ttt90) REVERT: I 53 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8098 (p0) outliers start: 74 outliers final: 58 residues processed: 182 average time/residue: 0.1905 time to fit residues: 48.5841 Evaluate side-chains 183 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 120 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 155 PHE Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 134 CYS Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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: 0.8265 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8863 Z= 0.371 Angle : 0.672 7.588 12094 Z= 0.346 Chirality : 0.046 0.161 1397 Planarity : 0.005 0.053 1541 Dihedral : 4.764 29.064 1241 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.31 % Favored : 85.17 % Rotamer: Outliers : 8.49 % Allowed : 28.45 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.98 (0.25), residues: 1153 helix: 0.32 (0.33), residues: 250 sheet: -1.17 (0.31), residues: 317 loop : -2.15 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.004 0.001 HIS B 119 PHE 0.015 0.002 PHE A 152 TYR 0.017 0.002 TYR B 180 ARG 0.006 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 121 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8098 (ptm160) REVERT: B 36 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8863 (mp) REVERT: B 207 ASP cc_start: 0.8518 (p0) cc_final: 0.8203 (p0) REVERT: B 348 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8802 (pp) REVERT: B 378 TRP cc_start: 0.8728 (OUTLIER) cc_final: 0.8135 (t60) REVERT: G 19 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8151 (mtp180) REVERT: I 53 ASN cc_start: 0.8414 (p0) cc_final: 0.8153 (p0) outliers start: 77 outliers final: 59 residues processed: 183 average time/residue: 0.1884 time to fit residues: 48.2620 Evaluate side-chains 181 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 117 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 6.9990 chunk 12 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 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: 0.8184 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8863 Z= 0.193 Angle : 0.607 7.537 12094 Z= 0.308 Chirality : 0.043 0.173 1397 Planarity : 0.004 0.052 1541 Dihedral : 4.429 22.010 1241 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.06 % Favored : 87.42 % Rotamer: Outliers : 7.06 % Allowed : 29.33 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.81 (0.25), residues: 1153 helix: 0.71 (0.33), residues: 250 sheet: -1.25 (0.30), residues: 325 loop : -2.06 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 284 HIS 0.003 0.001 HIS A 293 PHE 0.013 0.001 PHE B 253 TYR 0.012 0.001 TYR B 321 ARG 0.005 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 126 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8229 (ptm160) REVERT: A 162 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6682 (m90) REVERT: B 207 ASP cc_start: 0.8521 (p0) cc_final: 0.8039 (p0) REVERT: B 348 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8838 (pp) REVERT: B 378 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.7948 (t60) REVERT: G 19 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8247 (mtp180) REVERT: I 53 ASN cc_start: 0.8354 (p0) cc_final: 0.8105 (p0) outliers start: 64 outliers final: 51 residues processed: 178 average time/residue: 0.1939 time to fit residues: 48.0047 Evaluate side-chains 175 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 119 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 69 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8863 Z= 0.220 Angle : 0.624 7.542 12094 Z= 0.319 Chirality : 0.044 0.161 1397 Planarity : 0.004 0.051 1541 Dihedral : 4.419 21.765 1241 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.66 % Favored : 86.82 % Rotamer: Outliers : 6.39 % Allowed : 30.76 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.82 (0.25), residues: 1153 helix: 0.77 (0.34), residues: 245 sheet: -1.32 (0.30), residues: 324 loop : -2.04 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 284 HIS 0.009 0.001 HIS A 293 PHE 0.033 0.001 PHE B 186 TYR 0.026 0.001 TYR B 180 ARG 0.006 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 126 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8179 (ptm160) REVERT: B 207 ASP cc_start: 0.8393 (p0) cc_final: 0.7903 (p0) REVERT: B 348 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8830 (pp) REVERT: B 378 TRP cc_start: 0.8615 (OUTLIER) cc_final: 0.7951 (t60) REVERT: G 19 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8492 (mtp180) REVERT: I 53 ASN cc_start: 0.8363 (p0) cc_final: 0.8112 (p0) outliers start: 58 outliers final: 51 residues processed: 172 average time/residue: 0.1954 time to fit residues: 46.6564 Evaluate side-chains 177 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 122 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 155 PHE Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.8233 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8863 Z= 0.290 Angle : 0.660 9.554 12094 Z= 0.338 Chirality : 0.045 0.164 1397 Planarity : 0.005 0.050 1541 Dihedral : 4.585 25.111 1241 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.79 % Favored : 85.69 % Rotamer: Outliers : 6.62 % Allowed : 31.09 % Favored : 62.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.95 (0.25), residues: 1153 helix: 0.49 (0.33), residues: 253 sheet: -1.28 (0.30), residues: 317 loop : -2.14 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 284 HIS 0.005 0.001 HIS A 293 PHE 0.016 0.002 PHE G 68 TYR 0.026 0.002 TYR B 180 ARG 0.007 0.000 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 123 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8171 (ptm160) REVERT: A 162 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6714 (m90) REVERT: B 207 ASP cc_start: 0.8406 (p0) cc_final: 0.8080 (p0) REVERT: B 348 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8797 (pp) REVERT: B 378 TRP cc_start: 0.8693 (OUTLIER) cc_final: 0.8051 (t60) REVERT: G 19 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8253 (mtp180) REVERT: G 154 TYR cc_start: 0.6168 (p90) cc_final: 0.5593 (p90) REVERT: I 53 ASN cc_start: 0.8382 (p0) cc_final: 0.8168 (p0) outliers start: 60 outliers final: 52 residues processed: 169 average time/residue: 0.1919 time to fit residues: 45.6971 Evaluate side-chains 178 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 121 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.0010 overall best weight: 0.8390 ------------------------------------------------------------------------------- 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: 0.8181 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8863 Z= 0.201 Angle : 0.632 9.318 12094 Z= 0.319 Chirality : 0.043 0.159 1397 Planarity : 0.004 0.051 1541 Dihedral : 4.409 21.205 1241 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.32 % Favored : 87.16 % Rotamer: Outliers : 6.28 % Allowed : 31.75 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.84 (0.25), residues: 1153 helix: 0.74 (0.34), residues: 245 sheet: -1.35 (0.30), residues: 323 loop : -2.02 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 284 HIS 0.003 0.001 HIS B 332 PHE 0.015 0.001 PHE B 253 TYR 0.025 0.001 TYR B 180 ARG 0.006 0.000 ARG G 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 131 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8146 (ptm160) REVERT: A 162 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6749 (m90) REVERT: B 207 ASP cc_start: 0.8384 (p0) cc_final: 0.8046 (p0) REVERT: B 348 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8832 (pp) REVERT: B 378 TRP cc_start: 0.8604 (OUTLIER) cc_final: 0.7932 (t60) REVERT: G 154 TYR cc_start: 0.6108 (p90) cc_final: 0.5523 (p90) REVERT: I 53 ASN cc_start: 0.8359 (p0) cc_final: 0.8150 (p0) outliers start: 57 outliers final: 51 residues processed: 175 average time/residue: 0.1897 time to fit residues: 47.0437 Evaluate side-chains 181 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 126 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.151478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112472 restraints weight = 15576.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110372 restraints weight = 14792.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111470 restraints weight = 15996.968| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8863 Z= 0.179 Angle : 0.621 8.986 12094 Z= 0.312 Chirality : 0.043 0.151 1397 Planarity : 0.004 0.052 1541 Dihedral : 4.296 21.011 1241 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.88 % Favored : 87.60 % Rotamer: Outliers : 6.28 % Allowed : 32.08 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.72 (0.25), residues: 1153 helix: 0.92 (0.34), residues: 246 sheet: -1.18 (0.30), residues: 319 loop : -2.06 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 284 HIS 0.007 0.001 HIS A 293 PHE 0.014 0.001 PHE B 253 TYR 0.023 0.001 TYR B 180 ARG 0.007 0.000 ARG G 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2102.02 seconds wall clock time: 44 minutes 19.89 seconds (2659.89 seconds total)