Starting phenix.real_space_refine on Wed Feb 14 08:25:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vig_32008/02_2024/7vig_32008_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vig_32008/02_2024/7vig_32008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vig_32008/02_2024/7vig_32008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vig_32008/02_2024/7vig_32008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vig_32008/02_2024/7vig_32008_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vig_32008/02_2024/7vig_32008_updated.pdb" } resolution = 2.89 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= -0.002 sd= 0.051 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: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 5692 2.51 5 N 1508 2.21 5 O 1654 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 234": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8920 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1804 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "F" Number of atoms: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2245 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 6, 'TRANS': 273} Chain breaks: 2 Chain: "D" Number of atoms: 1804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 223, 1798 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 223, 1798 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 bond proxies already assigned to first conformer: 1820 Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'7I4': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS D 305 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 305 " occ=0.50 Time building chain proxies: 5.85, per 1000 atoms: 0.66 Number of scatterers: 8920 At special positions: 0 Unit cell: (92.13, 119.52, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 F 1 9.00 O 1654 8.00 N 1508 7.00 C 5692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 282 " - pdb=" SG CYS F 287 " 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: 3.14 Conformation dependent library (CDL) restraints added in 2.0 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 34.2% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 29 through 32 No H-bonds generated for 'chain 'A' and resid 29 through 32' Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'F' and resid 24 through 32 removed outlier: 3.779A pdb=" N THR F 32 " --> pdb=" O HIS F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 72 Processing helix chain 'F' and resid 79 through 104 Processing helix chain 'F' and resid 114 through 147 removed outlier: 3.922A pdb=" N MET F 124 " --> pdb=" O ARG F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 180 removed outlier: 3.832A pdb=" N SER F 171 " --> pdb=" O CYS F 167 " (cutoff:3.500A) Proline residue: F 178 - end of helix Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 200 through 234 Processing helix chain 'F' and resid 250 through 281 Proline residue: F 271 - end of helix removed outlier: 3.890A pdb=" N VAL F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 313 Proline residue: F 308 - end of helix Processing helix chain 'F' and resid 316 through 323 Processing helix chain 'D' and resid 7 through 32 removed outlier: 3.585A pdb=" N ARG D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 231 removed outlier: 3.907A pdb=" N ASP D 231 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.740A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 351 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 61 removed outlier: 6.896A pdb=" N ALA A 72 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET A 60 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 70 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP A 82 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS A 88 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 104 removed outlier: 6.874A pdb=" N GLY A 114 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS A 102 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA A 112 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TYR A 104 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR A 110 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY A 115 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN A 124 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL A 134 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.693A pdb=" N SER A 159 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 148 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 157 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE A 150 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLN A 155 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP A 169 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN A 175 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 186 through 191 removed outlier: 7.066A pdb=" N GLY A 201 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU A 189 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 199 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU A 191 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A 197 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 219 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP A 211 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS A 217 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 228 through 233 removed outlier: 6.709A pdb=" N GLY A 243 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 231 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 241 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE A 233 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA A 239 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASP A 253 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLU A 259 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 272 through 277 removed outlier: 6.631A pdb=" N GLY A 287 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A 275 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 285 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE A 277 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU A 283 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ASP A 297 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG A 303 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.653A pdb=" N ILE A 337 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR A 49 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 335 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.604A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.749A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL E 149 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU E 246 " --> pdb=" O VAL E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.517A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 225 through 231 removed outlier: 6.188A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ARG E 180 " --> pdb=" O PRO E 185 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 319 through 322 removed outlier: 6.607A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS D 195 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU D 36 " --> pdb=" O HIS D 195 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS D 197 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 38 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE D 199 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N GLY D 40 " --> pdb=" O PHE D 199 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1174 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: 2.30 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1435 1.29 - 1.42: 2399 1.42 - 1.55: 5170 1.55 - 1.68: 3 1.68 - 1.81: 92 Bond restraints: 9099 Sorted by residual: bond pdb=" C16 7I4 F 401 " pdb=" N17 7I4 F 401 " ideal model delta sigma weight residual 1.441 1.155 0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C18 7I4 F 401 " pdb=" C19 7I4 F 401 " ideal model delta sigma weight residual 1.533 1.410 0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C19 7I4 F 401 " pdb=" C23 7I4 F 401 " ideal model delta sigma weight residual 1.537 1.417 0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C11 7I4 F 401 " pdb=" C12 7I4 F 401 " ideal model delta sigma weight residual 1.462 1.576 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C08 7I4 F 401 " pdb=" C09 7I4 F 401 " ideal model delta sigma weight residual 1.452 1.546 -0.094 2.00e-02 2.50e+03 2.22e+01 ... (remaining 9094 not shown) Histogram of bond angle deviations from ideal: 89.03 - 99.04: 6 99.04 - 109.05: 568 109.05 - 119.06: 6896 119.06 - 129.07: 4775 129.07 - 139.07: 68 Bond angle restraints: 12313 Sorted by residual: angle pdb=" C12 7I4 F 401 " pdb=" C11 7I4 F 401 " pdb=" N10 7I4 F 401 " ideal model delta sigma weight residual 123.31 139.07 -15.76 3.00e+00 1.11e-01 2.76e+01 angle pdb=" C11 7I4 F 401 " pdb=" C12 7I4 F 401 " pdb=" C26 7I4 F 401 " ideal model delta sigma weight residual 119.29 132.36 -13.07 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " pdb=" CG TYR E 235 " ideal model delta sigma weight residual 113.90 106.09 7.81 1.80e+00 3.09e-01 1.88e+01 angle pdb=" C15 7I4 F 401 " pdb=" C16 7I4 F 401 " pdb=" N17 7I4 F 401 " ideal model delta sigma weight residual 110.91 122.57 -11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C08 7I4 F 401 " pdb=" C09 7I4 F 401 " pdb=" N10 7I4 F 401 " ideal model delta sigma weight residual 128.22 138.84 -10.62 3.00e+00 1.11e-01 1.25e+01 ... (remaining 12308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 4899 16.28 - 32.57: 402 32.57 - 48.85: 90 48.85 - 65.14: 11 65.14 - 81.42: 12 Dihedral angle restraints: 5414 sinusoidal: 2125 harmonic: 3289 Sorted by residual: dihedral pdb=" CA GLU E 234 " pdb=" C GLU E 234 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " ideal model delta harmonic sigma weight residual -180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CB CYS F 184 " pdb=" SG CYS F 184 " pdb=" SG CYS F 191 " pdb=" CB CYS F 191 " ideal model delta sinusoidal sigma weight residual -86.00 -126.20 40.20 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA MET D 240 " pdb=" C MET D 240 " pdb=" N ASN D 241 " pdb=" CA ASN D 241 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1386 0.118 - 0.236: 23 0.236 - 0.354: 0 0.354 - 0.472: 0 0.472 - 0.590: 1 Chirality restraints: 1410 Sorted by residual: chirality pdb=" C19 7I4 F 401 " pdb=" C18 7I4 F 401 " pdb=" C20 7I4 F 401 " pdb=" C23 7I4 F 401 " both_signs ideal model delta sigma weight residual False -2.88 -2.29 -0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CB ILE F 60 " pdb=" CA ILE F 60 " pdb=" CG1 ILE F 60 " pdb=" CG2 ILE F 60 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CG LEU F 136 " pdb=" CB LEU F 136 " pdb=" CD1 LEU F 136 " pdb=" CD2 LEU F 136 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 1407 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 235 " 0.030 2.00e-02 2.50e+03 1.76e-02 6.23e+00 pdb=" CG TYR E 235 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 235 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR E 235 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR E 235 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 235 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR E 235 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 235 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO E 236 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 113 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO F 114 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 114 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 114 " 0.026 5.00e-02 4.00e+02 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 818 2.74 - 3.28: 8878 3.28 - 3.82: 15112 3.82 - 4.36: 18634 4.36 - 4.90: 32685 Nonbonded interactions: 76127 Sorted by model distance: nonbonded pdb=" O LEU F 174 " pdb=" OH TYR F 202 " model vdw 2.203 2.440 nonbonded pdb=" OD1 ASP D 251 " pdb=" ND2 ASN D 255 " model vdw 2.209 2.520 nonbonded pdb=" OE2 GLU D 318 " pdb=" OH TYR D 320 " model vdw 2.212 2.440 nonbonded pdb=" OD2 ASP A 227 " pdb=" NZ LYS D 209 " model vdw 2.221 2.520 nonbonded pdb=" OG1 THR A 273 " pdb=" O VAL A 314 " model vdw 2.224 2.440 ... (remaining 76122 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=0.50 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.550 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.130 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.006 0.286 9099 Z= 0.387 Angle : 0.712 15.764 12313 Z= 0.348 Chirality : 0.047 0.590 1410 Planarity : 0.004 0.049 1539 Dihedral : 13.094 81.421 3280 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1116 helix: 1.92 (0.25), residues: 391 sheet: 0.48 (0.31), residues: 274 loop : -0.46 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 81 HIS 0.006 0.001 HIS A 141 PHE 0.014 0.001 PHE D 189 TYR 0.038 0.002 TYR E 235 ARG 0.005 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.607 Fit side-chains REVERT: E 34 MET cc_start: 0.8934 (mmm) cc_final: 0.8672 (mmt) REVERT: D 272 ASP cc_start: 0.7085 (m-30) cc_final: 0.6781 (m-30) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 1.2281 time to fit residues: 186.4473 Evaluate side-chains 111 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN F 303 ASN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 0.028 9099 Z= 0.202 Angle : 0.563 9.033 12313 Z= 0.280 Chirality : 0.042 0.223 1410 Planarity : 0.004 0.056 1539 Dihedral : 6.189 65.515 1243 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.74 % Allowed : 8.60 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1116 helix: 2.14 (0.25), residues: 391 sheet: 0.37 (0.29), residues: 279 loop : -0.46 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 81 HIS 0.005 0.001 HIS A 141 PHE 0.012 0.001 PHE D 189 TYR 0.034 0.001 TYR E 235 ARG 0.005 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.044 Fit side-chains REVERT: A 216 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7430 (ppp) REVERT: E 186 GLN cc_start: 0.8254 (tt0) cc_final: 0.8019 (tt0) REVERT: E 230 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7280 (ttt) outliers start: 17 outliers final: 7 residues processed: 124 average time/residue: 1.0734 time to fit residues: 143.7227 Evaluate side-chains 117 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 100 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 77 ASN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9099 Z= 0.164 Angle : 0.511 7.578 12313 Z= 0.259 Chirality : 0.041 0.220 1410 Planarity : 0.004 0.054 1539 Dihedral : 5.555 53.145 1243 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.46 % Allowed : 11.46 % Favored : 86.08 % 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: 1.10 (0.25), residues: 1116 helix: 2.28 (0.25), residues: 392 sheet: 0.38 (0.29), residues: 279 loop : -0.40 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 81 HIS 0.004 0.001 HIS A 141 PHE 0.014 0.001 PHE D 189 TYR 0.034 0.001 TYR E 235 ARG 0.007 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8248 (mpt-90) REVERT: A 216 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7352 (ppp) REVERT: F 177 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7793 (mp) REVERT: F 292 ARG cc_start: 0.7493 (mpp80) cc_final: 0.6926 (mtt90) REVERT: F 318 MET cc_start: 0.8474 (tpt) cc_final: 0.8272 (tpt) REVERT: D 330 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7805 (mtmt) outliers start: 24 outliers final: 13 residues processed: 131 average time/residue: 1.1487 time to fit residues: 161.5360 Evaluate side-chains 128 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 330 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 186 GLN D 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9099 Z= 0.180 Angle : 0.499 7.263 12313 Z= 0.256 Chirality : 0.041 0.219 1410 Planarity : 0.004 0.055 1539 Dihedral : 4.981 36.497 1243 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.35 % Allowed : 12.90 % Favored : 84.75 % 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: 1.15 (0.25), residues: 1116 helix: 2.36 (0.25), residues: 392 sheet: 0.40 (0.29), residues: 279 loop : -0.41 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 81 HIS 0.004 0.001 HIS A 141 PHE 0.012 0.001 PHE D 189 TYR 0.037 0.001 TYR E 235 ARG 0.007 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8205 (mpt-90) REVERT: A 216 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7332 (ppp) REVERT: C 20 LYS cc_start: 0.8177 (mttp) cc_final: 0.7932 (ttmm) REVERT: F 177 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8107 (mt) REVERT: F 292 ARG cc_start: 0.7487 (mpp80) cc_final: 0.6894 (mtt90) REVERT: D 330 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7847 (mtmt) outliers start: 23 outliers final: 15 residues processed: 129 average time/residue: 1.1886 time to fit residues: 164.7002 Evaluate side-chains 130 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 330 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.0670 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9099 Z= 0.146 Angle : 0.471 7.126 12313 Z= 0.245 Chirality : 0.040 0.199 1410 Planarity : 0.004 0.054 1539 Dihedral : 4.503 30.757 1243 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.25 % Allowed : 13.82 % Favored : 83.93 % 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: 1.18 (0.25), residues: 1116 helix: 2.42 (0.25), residues: 391 sheet: 0.42 (0.29), residues: 274 loop : -0.42 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 81 HIS 0.003 0.001 HIS A 141 PHE 0.014 0.001 PHE D 189 TYR 0.033 0.001 TYR E 235 ARG 0.008 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8236 (mpt-90) REVERT: C 20 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7918 (ttmm) REVERT: F 177 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8062 (mt) REVERT: F 292 ARG cc_start: 0.7492 (mpp80) cc_final: 0.6889 (mtt90) REVERT: D 330 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7817 (mtmt) outliers start: 22 outliers final: 16 residues processed: 132 average time/residue: 1.1220 time to fit residues: 159.3118 Evaluate side-chains 135 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 330 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.0670 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 186 GLN D 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9099 Z= 0.175 Angle : 0.478 7.419 12313 Z= 0.250 Chirality : 0.041 0.238 1410 Planarity : 0.004 0.055 1539 Dihedral : 4.417 28.051 1243 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.76 % Allowed : 13.92 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1116 helix: 2.40 (0.25), residues: 391 sheet: 0.42 (0.30), residues: 274 loop : -0.42 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 81 HIS 0.004 0.001 HIS A 141 PHE 0.011 0.001 PHE D 189 TYR 0.036 0.001 TYR E 235 ARG 0.008 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8200 (mpt-90) REVERT: F 177 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8089 (mt) REVERT: F 292 ARG cc_start: 0.7518 (mpp80) cc_final: 0.6806 (mtm-85) REVERT: D 330 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7823 (mtmt) outliers start: 27 outliers final: 18 residues processed: 130 average time/residue: 1.1392 time to fit residues: 158.9204 Evaluate side-chains 133 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 330 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 186 GLN D 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9099 Z= 0.291 Angle : 0.545 7.825 12313 Z= 0.284 Chirality : 0.043 0.250 1410 Planarity : 0.004 0.053 1539 Dihedral : 4.942 31.477 1243 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.56 % Allowed : 14.74 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1116 helix: 2.14 (0.25), residues: 392 sheet: 0.34 (0.30), residues: 276 loop : -0.47 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.006 0.001 HIS A 141 PHE 0.013 0.001 PHE D 189 TYR 0.044 0.002 TYR E 235 ARG 0.009 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8128 (mpt-90) REVERT: A 216 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7425 (ppp) REVERT: C 20 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8351 (mtpp) REVERT: F 177 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7820 (mp) REVERT: F 292 ARG cc_start: 0.7518 (mpp80) cc_final: 0.6798 (mtm-85) REVERT: D 243 MET cc_start: 0.8039 (ttp) cc_final: 0.7736 (mtm) outliers start: 25 outliers final: 17 residues processed: 122 average time/residue: 1.1708 time to fit residues: 153.6149 Evaluate side-chains 128 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.0010 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.0570 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.7908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9099 Z= 0.186 Angle : 0.496 7.968 12313 Z= 0.259 Chirality : 0.041 0.271 1410 Planarity : 0.004 0.052 1539 Dihedral : 4.617 29.235 1243 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.15 % Allowed : 15.76 % Favored : 82.09 % 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: 1.04 (0.25), residues: 1116 helix: 2.24 (0.25), residues: 392 sheet: 0.41 (0.30), residues: 274 loop : -0.48 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 81 HIS 0.004 0.001 HIS A 141 PHE 0.013 0.001 PHE D 189 TYR 0.025 0.001 TYR E 235 ARG 0.010 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8140 (mpt-90) REVERT: A 213 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7922 (mmt90) REVERT: C 20 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8351 (mtpp) REVERT: F 177 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8057 (mt) REVERT: F 292 ARG cc_start: 0.7536 (mpp80) cc_final: 0.6812 (mtm-85) REVERT: D 243 MET cc_start: 0.7969 (ttp) cc_final: 0.7708 (mtm) outliers start: 21 outliers final: 15 residues processed: 124 average time/residue: 1.1551 time to fit residues: 154.3179 Evaluate side-chains 125 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9099 Z= 0.164 Angle : 0.486 8.081 12313 Z= 0.252 Chirality : 0.041 0.275 1410 Planarity : 0.004 0.053 1539 Dihedral : 4.407 26.631 1243 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.35 % Allowed : 15.35 % Favored : 82.29 % 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: 1.12 (0.25), residues: 1116 helix: 2.33 (0.25), residues: 390 sheet: 0.41 (0.30), residues: 281 loop : -0.44 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 81 HIS 0.004 0.001 HIS A 141 PHE 0.012 0.001 PHE D 189 TYR 0.024 0.001 TYR E 235 ARG 0.010 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8171 (mpt-90) REVERT: A 213 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7928 (mmt90) REVERT: F 135 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8343 (mp) REVERT: F 177 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8010 (mt) REVERT: D 243 MET cc_start: 0.7936 (ttp) cc_final: 0.7647 (mtm) outliers start: 23 outliers final: 17 residues processed: 127 average time/residue: 1.1761 time to fit residues: 160.1956 Evaluate side-chains 130 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 0.0570 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 258 GLN E 186 GLN F 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9099 Z= 0.243 Angle : 0.532 9.872 12313 Z= 0.274 Chirality : 0.042 0.270 1410 Planarity : 0.004 0.055 1539 Dihedral : 4.675 28.584 1243 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.56 % Allowed : 15.86 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1116 helix: 2.19 (0.25), residues: 392 sheet: 0.34 (0.30), residues: 284 loop : -0.44 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.005 0.001 HIS A 141 PHE 0.013 0.001 PHE D 189 TYR 0.027 0.002 TYR E 235 ARG 0.011 0.000 ARG F 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8180 (mpt-90) REVERT: A 213 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7971 (mmt90) REVERT: C 20 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8398 (mtpp) REVERT: F 135 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8350 (mp) REVERT: F 177 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8015 (mt) outliers start: 25 outliers final: 18 residues processed: 128 average time/residue: 1.1015 time to fit residues: 151.7580 Evaluate side-chains 131 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.103468 restraints weight = 21342.863| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.69 r_work: 0.3012 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9099 Z= 0.176 Angle : 0.502 9.732 12313 Z= 0.259 Chirality : 0.041 0.273 1410 Planarity : 0.004 0.054 1539 Dihedral : 4.473 27.272 1243 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.84 % Allowed : 17.09 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1116 helix: 2.26 (0.25), residues: 392 sheet: 0.41 (0.30), residues: 281 loop : -0.44 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 81 HIS 0.004 0.001 HIS A 141 PHE 0.012 0.001 PHE D 189 TYR 0.026 0.001 TYR E 235 ARG 0.011 0.000 ARG F 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3446.47 seconds wall clock time: 62 minutes 15.72 seconds (3735.72 seconds total)