Starting phenix.real_space_refine on Sat Dec 28 14:06:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eja_31157/12_2024/7eja_31157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eja_31157/12_2024/7eja_31157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eja_31157/12_2024/7eja_31157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eja_31157/12_2024/7eja_31157.map" model { file = "/net/cci-nas-00/data/ceres_data/7eja_31157/12_2024/7eja_31157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eja_31157/12_2024/7eja_31157.cif" } resolution = 3.6 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= -0.007 sd= 0.192 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 58 5.16 5 C 5487 2.51 5 N 1458 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8584 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1632 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 198} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2541 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2193 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1785 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CZX': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 5.30, per 1000 atoms: 0.62 Number of scatterers: 8584 At special positions: 0 Unit cell: (88.4, 120.7, 124.95, 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 58 16.00 O 1581 8.00 N 1458 7.00 C 5487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 34.7% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.682A pdb=" N ARG A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.207A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 4.170A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 245 through 256 removed outlier: 4.213A pdb=" N MET A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.100A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 329 through 350 removed outlier: 4.482A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.591A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.802A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'R' and resid 47 through 74 Processing helix chain 'R' and resid 83 through 108 removed outlier: 4.473A pdb=" N LEU R 87 " --> pdb=" O GLN R 83 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 120 through 151 Processing helix chain 'R' and resid 152 through 157 Processing helix chain 'R' and resid 158 through 160 No H-bonds generated for 'chain 'R' and resid 158 through 160' Processing helix chain 'R' and resid 161 through 181 Processing helix chain 'R' and resid 208 through 242 removed outlier: 3.683A pdb=" N ILE R 213 " --> pdb=" O LYS R 209 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER R 214 " --> pdb=" O TRP R 210 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ALA R 222 " --> pdb=" O GLY R 218 " (cutoff:3.500A) Proline residue: R 223 - end of helix Processing helix chain 'R' and resid 376 through 411 removed outlier: 3.698A pdb=" N ASN R 382 " --> pdb=" O ARG R 378 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE R 398 " --> pdb=" O VAL R 394 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL R 399 " --> pdb=" O ILE R 395 " (cutoff:3.500A) Proline residue: R 404 - end of helix Processing helix chain 'R' and resid 422 through 443 removed outlier: 3.775A pdb=" N GLY R 430 " --> pdb=" O PHE R 426 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR R 431 " --> pdb=" O PHE R 427 " (cutoff:3.500A) Proline residue: R 438 - end of helix removed outlier: 3.543A pdb=" N TYR R 441 " --> pdb=" O ASN R 437 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 457 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.762A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.862A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 201 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.967A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.931A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.306A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.615A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.679A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.599A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.804A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.464A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.847A pdb=" N GLU H 234 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU H 162 " --> pdb=" O TYR H 178 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR H 178 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU H 176 " --> pdb=" O TRP H 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 143 through 148 removed outlier: 3.952A pdb=" N PHE H 200 " --> pdb=" O CYS H 147 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1035 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: 2.29 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1385 1.31 - 1.44: 2457 1.44 - 1.56: 4847 1.56 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8768 Sorted by residual: bond pdb=" N ILE R 123 " pdb=" CA ILE R 123 " ideal model delta sigma weight residual 1.461 1.396 0.065 1.17e-02 7.31e+03 3.07e+01 bond pdb=" N ASN A 346 " pdb=" CA ASN A 346 " ideal model delta sigma weight residual 1.459 1.400 0.060 1.20e-02 6.94e+03 2.47e+01 bond pdb=" CA TYR R 156 " pdb=" C TYR R 156 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.29e-02 6.01e+03 2.45e+01 bond pdb=" CA ASN A 346 " pdb=" C ASN A 346 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.26e-02 6.30e+03 2.30e+01 bond pdb=" N PRO R 438 " pdb=" CD PRO R 438 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.22e+01 ... (remaining 8763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 11697 2.88 - 5.76: 148 5.76 - 8.64: 27 8.64 - 11.53: 6 11.53 - 14.41: 3 Bond angle restraints: 11881 Sorted by residual: angle pdb=" N ARG R 378 " pdb=" CA ARG R 378 " pdb=" C ARG R 378 " ideal model delta sigma weight residual 111.28 121.19 -9.91 1.09e+00 8.42e-01 8.27e+01 angle pdb=" N LYS A 211 " pdb=" CA LYS A 211 " pdb=" C LYS A 211 " ideal model delta sigma weight residual 111.14 119.75 -8.61 1.08e+00 8.57e-01 6.36e+01 angle pdb=" N HIS A 214 " pdb=" CA HIS A 214 " pdb=" C HIS A 214 " ideal model delta sigma weight residual 111.28 119.83 -8.55 1.09e+00 8.42e-01 6.16e+01 angle pdb=" N LYS R 159 " pdb=" CA LYS R 159 " pdb=" C LYS R 159 " ideal model delta sigma weight residual 113.15 122.41 -9.26 1.19e+00 7.06e-01 6.06e+01 angle pdb=" N CYS R 121 " pdb=" CA CYS R 121 " pdb=" C CYS R 121 " ideal model delta sigma weight residual 112.90 103.56 9.34 1.31e+00 5.83e-01 5.08e+01 ... (remaining 11876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.99: 5081 33.99 - 67.98: 90 67.98 - 101.97: 9 101.97 - 135.95: 0 135.95 - 169.94: 2 Dihedral angle restraints: 5182 sinusoidal: 2004 harmonic: 3178 Sorted by residual: dihedral pdb=" N ILE R 123 " pdb=" C ILE R 123 " pdb=" CA ILE R 123 " pdb=" CB ILE R 123 " ideal model delta harmonic sigma weight residual 123.40 109.48 13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" C PHE A 216 " pdb=" N PHE A 216 " pdb=" CA PHE A 216 " pdb=" CB PHE A 216 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" CA ILE G 25 " pdb=" C ILE G 25 " pdb=" N ASP G 26 " pdb=" CA ASP G 26 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 5179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1292 0.110 - 0.219: 39 0.219 - 0.329: 12 0.329 - 0.438: 4 0.438 - 0.548: 2 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA PHE A 216 " pdb=" N PHE A 216 " pdb=" C PHE A 216 " pdb=" CB PHE A 216 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" CA GLU A 217 " pdb=" N GLU A 217 " pdb=" C GLU A 217 " pdb=" CB GLU A 217 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA LYS R 159 " pdb=" N LYS R 159 " pdb=" C LYS R 159 " pdb=" CB LYS R 159 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 1346 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 161 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO R 162 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 162 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 162 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 183 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C THR A 183 " -0.034 2.00e-02 2.50e+03 pdb=" O THR A 183 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 184 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 282 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A 283 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.026 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 68 2.49 - 3.10: 6396 3.10 - 3.70: 13194 3.70 - 4.30: 17548 4.30 - 4.90: 28824 Nonbonded interactions: 66030 Sorted by model distance: nonbonded pdb=" OE1 GLN R 83 " pdb=" NH2 ARG R 160 " model vdw 1.893 3.120 nonbonded pdb=" O PHE A 224 " pdb=" N PHE A 268 " model vdw 1.959 3.120 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.175 3.040 nonbonded pdb=" OG SER H 192 " pdb=" OG1 THR H 203 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.224 3.040 ... (remaining 66025 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.390 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8768 Z= 0.292 Angle : 0.850 14.408 11881 Z= 0.537 Chirality : 0.059 0.548 1349 Planarity : 0.004 0.055 1496 Dihedral : 13.816 169.942 3121 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.11 % Allowed : 0.75 % Favored : 99.14 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.43 (0.26), residues: 1075 helix: 1.20 (0.28), residues: 341 sheet: -0.37 (0.33), residues: 263 loop : -1.32 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS A 189 PHE 0.022 0.001 PHE R 398 TYR 0.013 0.001 TYR R 156 ARG 0.005 0.000 ARG R 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8705 (mmm-85) REVERT: B 36 ASN cc_start: 0.8672 (m-40) cc_final: 0.8362 (p0) REVERT: B 255 LEU cc_start: 0.9382 (pt) cc_final: 0.9117 (mm) REVERT: B 261 LEU cc_start: 0.9371 (mt) cc_final: 0.9168 (mt) REVERT: B 280 LYS cc_start: 0.9349 (tptp) cc_final: 0.9026 (tptp) REVERT: B 292 PHE cc_start: 0.7801 (m-10) cc_final: 0.7482 (m-10) REVERT: G 21 MET cc_start: 0.8107 (mmp) cc_final: 0.7295 (mtm) REVERT: G 32 LYS cc_start: 0.9511 (ptpp) cc_final: 0.9293 (ptmm) REVERT: G 42 GLU cc_start: 0.8135 (tp30) cc_final: 0.7530 (mt-10) REVERT: G 58 GLU cc_start: 0.8998 (mp0) cc_final: 0.8428 (mp0) REVERT: R 53 CYS cc_start: 0.9179 (m) cc_final: 0.8880 (p) REVERT: R 57 LEU cc_start: 0.9416 (tp) cc_final: 0.9184 (tp) REVERT: R 109 GLU cc_start: 0.8887 (tp30) cc_final: 0.8314 (tm-30) REVERT: R 450 ARG cc_start: 0.9489 (mtm110) cc_final: 0.9216 (mtm-85) REVERT: H 46 GLU cc_start: 0.8579 (pt0) cc_final: 0.8189 (pm20) REVERT: H 90 ASP cc_start: 0.8059 (m-30) cc_final: 0.7532 (m-30) REVERT: H 137 VAL cc_start: 0.7359 (m) cc_final: 0.7129 (m) REVERT: H 180 MET cc_start: 0.8772 (ppp) cc_final: 0.8273 (ppp) REVERT: H 210 GLU cc_start: 0.8971 (mp0) cc_final: 0.8577 (mp0) REVERT: H 211 ASP cc_start: 0.7848 (m-30) cc_final: 0.7330 (m-30) REVERT: H 218 MET cc_start: 0.8712 (tmm) cc_final: 0.8146 (tmm) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.2444 time to fit residues: 73.8543 Evaluate side-chains 152 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 9.9990 chunk 81 optimal weight: 0.0970 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 50.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 266 HIS R 138 HIS R 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8768 Z= 0.175 Angle : 0.701 10.669 11881 Z= 0.359 Chirality : 0.045 0.163 1349 Planarity : 0.004 0.056 1496 Dihedral : 7.970 162.677 1193 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.61 % Allowed : 11.94 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.12 (0.26), residues: 1075 helix: 1.51 (0.28), residues: 340 sheet: -0.06 (0.34), residues: 254 loop : -1.26 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS B 225 PHE 0.028 0.001 PHE R 387 TYR 0.028 0.001 TYR R 156 ARG 0.006 0.000 ARG H 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8600 (tm-30) REVERT: A 244 MET cc_start: 0.5280 (mpp) cc_final: 0.4844 (mpp) REVERT: A 313 ARG cc_start: 0.8873 (mmm160) cc_final: 0.8644 (mmm-85) REVERT: A 320 TYR cc_start: 0.8389 (m-80) cc_final: 0.8115 (m-80) REVERT: A 354 TYR cc_start: 0.8532 (p90) cc_final: 0.8283 (p90) REVERT: B 12 GLU cc_start: 0.9314 (pt0) cc_final: 0.8986 (pm20) REVERT: B 17 GLN cc_start: 0.7375 (tm-30) cc_final: 0.7090 (pp30) REVERT: B 59 TYR cc_start: 0.8245 (m-80) cc_final: 0.7908 (m-80) REVERT: B 292 PHE cc_start: 0.7678 (m-10) cc_final: 0.7413 (m-10) REVERT: G 21 MET cc_start: 0.8060 (mmp) cc_final: 0.7338 (mtm) REVERT: G 32 LYS cc_start: 0.9432 (ptpp) cc_final: 0.9221 (ptmm) REVERT: G 38 MET cc_start: 0.6559 (ptp) cc_final: 0.5712 (ptt) REVERT: G 42 GLU cc_start: 0.8099 (tp30) cc_final: 0.7468 (mt-10) REVERT: G 58 GLU cc_start: 0.9034 (mp0) cc_final: 0.8507 (mp0) REVERT: R 53 CYS cc_start: 0.9126 (m) cc_final: 0.8823 (p) REVERT: R 94 ASP cc_start: 0.8279 (t70) cc_final: 0.7430 (t70) REVERT: R 95 ILE cc_start: 0.9698 (mm) cc_final: 0.9471 (mm) REVERT: R 109 GLU cc_start: 0.8799 (tp30) cc_final: 0.8258 (tm-30) REVERT: R 381 GLN cc_start: 0.9031 (pt0) cc_final: 0.8520 (pt0) REVERT: R 446 HIS cc_start: 0.9023 (OUTLIER) cc_final: 0.8754 (t70) REVERT: H 34 MET cc_start: 0.8549 (tpp) cc_final: 0.8323 (tpp) REVERT: H 180 MET cc_start: 0.8823 (ppp) cc_final: 0.8367 (ppp) REVERT: H 190 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.5218 (ptm160) REVERT: H 208 GLU cc_start: 0.8369 (pt0) cc_final: 0.8155 (pm20) REVERT: H 211 ASP cc_start: 0.7655 (m-30) cc_final: 0.6718 (m-30) REVERT: H 218 MET cc_start: 0.8639 (tmm) cc_final: 0.8308 (tmm) outliers start: 15 outliers final: 10 residues processed: 199 average time/residue: 0.2350 time to fit residues: 62.4306 Evaluate side-chains 168 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 40.0000 chunk 106 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 256 ASN A 333 GLN R 138 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8768 Z= 0.325 Angle : 0.735 11.307 11881 Z= 0.380 Chirality : 0.045 0.144 1349 Planarity : 0.004 0.050 1496 Dihedral : 8.065 161.904 1193 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.90 % Allowed : 16.77 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.14 (0.26), residues: 1075 helix: 1.57 (0.28), residues: 339 sheet: -0.14 (0.33), residues: 269 loop : -1.32 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.013 0.002 HIS R 138 PHE 0.019 0.002 PHE R 387 TYR 0.024 0.002 TYR R 409 ARG 0.006 0.001 ARG R 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8977 (mmm160) cc_final: 0.8752 (mmm-85) REVERT: A 320 TYR cc_start: 0.8265 (m-80) cc_final: 0.7414 (m-80) REVERT: B 12 GLU cc_start: 0.9309 (pt0) cc_final: 0.8974 (pm20) REVERT: B 36 ASN cc_start: 0.8588 (m-40) cc_final: 0.8277 (p0) REVERT: B 232 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8571 (tt) REVERT: B 292 PHE cc_start: 0.8180 (m-10) cc_final: 0.7749 (m-10) REVERT: G 38 MET cc_start: 0.6641 (ptp) cc_final: 0.6262 (ptt) REVERT: G 42 GLU cc_start: 0.8173 (tp30) cc_final: 0.7662 (mt-10) REVERT: G 58 GLU cc_start: 0.9115 (mp0) cc_final: 0.8564 (mp0) REVERT: R 53 CYS cc_start: 0.9165 (m) cc_final: 0.8964 (m) REVERT: R 94 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7429 (t70) REVERT: R 109 GLU cc_start: 0.8936 (tp30) cc_final: 0.8302 (tm-30) REVERT: R 446 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8676 (t70) REVERT: H 180 MET cc_start: 0.8821 (ppp) cc_final: 0.8374 (ppp) REVERT: H 218 MET cc_start: 0.8691 (tmm) cc_final: 0.8472 (tmm) outliers start: 27 outliers final: 18 residues processed: 168 average time/residue: 0.2181 time to fit residues: 50.1499 Evaluate side-chains 155 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 89 SER Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 446 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 30.0000 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 65 optimal weight: 0.0970 chunk 98 optimal weight: 40.0000 chunk 104 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN R 138 HIS R 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8768 Z= 0.219 Angle : 0.707 11.946 11881 Z= 0.356 Chirality : 0.043 0.146 1349 Planarity : 0.004 0.050 1496 Dihedral : 8.001 161.941 1193 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.76 % Allowed : 17.31 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.08 (0.26), residues: 1075 helix: 1.62 (0.28), residues: 338 sheet: -0.02 (0.33), residues: 262 loop : -1.32 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.007 0.001 HIS R 138 PHE 0.021 0.001 PHE R 387 TYR 0.023 0.001 TYR R 409 ARG 0.004 0.000 ARG H 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8969 (mmm160) cc_final: 0.8748 (mmm-85) REVERT: B 12 GLU cc_start: 0.9299 (pt0) cc_final: 0.8959 (pm20) REVERT: B 17 GLN cc_start: 0.7438 (tm-30) cc_final: 0.7101 (pp30) REVERT: B 36 ASN cc_start: 0.8560 (m-40) cc_final: 0.8230 (p0) REVERT: B 232 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8558 (tt) REVERT: B 292 PHE cc_start: 0.8135 (m-10) cc_final: 0.7744 (m-10) REVERT: G 21 MET cc_start: 0.8421 (mmm) cc_final: 0.7357 (mtm) REVERT: G 38 MET cc_start: 0.6758 (ptp) cc_final: 0.6043 (ptt) REVERT: G 42 GLU cc_start: 0.8143 (tp30) cc_final: 0.7534 (mt-10) REVERT: G 58 GLU cc_start: 0.9127 (mp0) cc_final: 0.8567 (mp0) REVERT: R 49 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7136 (pt) REVERT: R 53 CYS cc_start: 0.9156 (m) cc_final: 0.8931 (m) REVERT: R 94 ASP cc_start: 0.8199 (t70) cc_final: 0.7338 (t70) REVERT: R 95 ILE cc_start: 0.9692 (mm) cc_final: 0.9427 (mm) REVERT: R 109 GLU cc_start: 0.8784 (tp30) cc_final: 0.8217 (tm-30) REVERT: R 204 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8826 (tm-30) REVERT: R 446 HIS cc_start: 0.9004 (OUTLIER) cc_final: 0.8724 (t70) REVERT: R 450 ARG cc_start: 0.9481 (mtm110) cc_final: 0.9281 (mtm110) REVERT: H 218 MET cc_start: 0.8729 (tmm) cc_final: 0.8525 (tmm) outliers start: 35 outliers final: 25 residues processed: 181 average time/residue: 0.2246 time to fit residues: 55.3216 Evaluate side-chains 169 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 89 SER Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 176 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8768 Z= 0.331 Angle : 0.758 11.896 11881 Z= 0.386 Chirality : 0.045 0.186 1349 Planarity : 0.004 0.047 1496 Dihedral : 8.077 160.063 1193 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.66 % Allowed : 19.46 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.29 (0.26), residues: 1075 helix: 1.52 (0.28), residues: 336 sheet: -0.28 (0.32), residues: 269 loop : -1.40 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.008 0.001 HIS B 225 PHE 0.019 0.002 PHE R 387 TYR 0.026 0.002 TYR A 320 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8805 (mm) cc_final: 0.8388 (mm) REVERT: A 313 ARG cc_start: 0.8996 (mmm160) cc_final: 0.8777 (mmm-85) REVERT: B 12 GLU cc_start: 0.9294 (pt0) cc_final: 0.8952 (pm20) REVERT: B 36 ASN cc_start: 0.8555 (m-40) cc_final: 0.8262 (p0) REVERT: B 59 TYR cc_start: 0.8455 (m-80) cc_final: 0.8223 (m-80) REVERT: B 232 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8612 (tt) REVERT: B 292 PHE cc_start: 0.8409 (m-10) cc_final: 0.8070 (m-80) REVERT: G 24 ASN cc_start: 0.7762 (t0) cc_final: 0.7169 (m-40) REVERT: G 38 MET cc_start: 0.6730 (ptp) cc_final: 0.6139 (ptt) REVERT: G 42 GLU cc_start: 0.8170 (tp30) cc_final: 0.7580 (mt-10) REVERT: G 58 GLU cc_start: 0.9170 (mp0) cc_final: 0.8477 (mp0) REVERT: R 49 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7177 (pt) REVERT: R 53 CYS cc_start: 0.9145 (m) cc_final: 0.8922 (m) REVERT: R 109 GLU cc_start: 0.8825 (tp30) cc_final: 0.8270 (tm-30) REVERT: R 446 HIS cc_start: 0.8963 (OUTLIER) cc_final: 0.8690 (t70) REVERT: R 448 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8783 (t80) REVERT: H 190 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.5752 (ptm160) REVERT: H 218 MET cc_start: 0.8744 (tmm) cc_final: 0.8515 (tmm) outliers start: 34 outliers final: 26 residues processed: 169 average time/residue: 0.2226 time to fit residues: 51.4805 Evaluate side-chains 167 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 448 PHE Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 104 optimal weight: 40.0000 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8768 Z= 0.237 Angle : 0.745 12.799 11881 Z= 0.371 Chirality : 0.043 0.188 1349 Planarity : 0.004 0.049 1496 Dihedral : 7.953 157.727 1193 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.55 % Allowed : 20.22 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.29 (0.26), residues: 1075 helix: 1.41 (0.28), residues: 341 sheet: -0.24 (0.32), residues: 266 loop : -1.36 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS B 225 PHE 0.022 0.001 PHE R 387 TYR 0.023 0.002 TYR A 354 ARG 0.004 0.000 ARG R 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8391 (mm) REVERT: A 313 ARG cc_start: 0.8972 (mmm160) cc_final: 0.8761 (mmm-85) REVERT: B 12 GLU cc_start: 0.9297 (pt0) cc_final: 0.8965 (pm20) REVERT: B 36 ASN cc_start: 0.8612 (m-40) cc_final: 0.8264 (p0) REVERT: B 232 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8607 (tt) REVERT: B 283 ARG cc_start: 0.7666 (ttt180) cc_final: 0.7344 (ttt180) REVERT: B 292 PHE cc_start: 0.8342 (m-10) cc_final: 0.7995 (m-80) REVERT: G 21 MET cc_start: 0.8360 (mmm) cc_final: 0.7321 (mtm) REVERT: G 24 ASN cc_start: 0.7728 (t0) cc_final: 0.7164 (m-40) REVERT: G 38 MET cc_start: 0.6645 (ptp) cc_final: 0.6089 (ptt) REVERT: G 42 GLU cc_start: 0.8147 (tp30) cc_final: 0.7585 (mt-10) REVERT: G 58 GLU cc_start: 0.9170 (mp0) cc_final: 0.8626 (mp0) REVERT: R 49 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7122 (pt) REVERT: R 53 CYS cc_start: 0.9126 (m) cc_final: 0.8890 (m) REVERT: R 94 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7433 (t70) REVERT: R 109 GLU cc_start: 0.8796 (tp30) cc_final: 0.8266 (tm-30) REVERT: R 446 HIS cc_start: 0.9022 (OUTLIER) cc_final: 0.8696 (t70) REVERT: R 448 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8744 (t80) REVERT: H 34 MET cc_start: 0.8584 (tpp) cc_final: 0.8299 (tpp) REVERT: H 190 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.5687 (ptm160) REVERT: H 218 MET cc_start: 0.8758 (tmm) cc_final: 0.8511 (tmm) outliers start: 33 outliers final: 23 residues processed: 178 average time/residue: 0.2148 time to fit residues: 52.3539 Evaluate side-chains 171 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 448 PHE Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8768 Z= 0.179 Angle : 0.744 13.830 11881 Z= 0.365 Chirality : 0.043 0.191 1349 Planarity : 0.004 0.051 1496 Dihedral : 7.757 154.648 1193 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.44 % Allowed : 20.97 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.16 (0.26), residues: 1075 helix: 1.62 (0.29), residues: 330 sheet: -0.07 (0.34), residues: 244 loop : -1.33 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 148 HIS 0.005 0.001 HIS A 196 PHE 0.018 0.001 PHE R 387 TYR 0.015 0.001 TYR R 156 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 313 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8676 (mmm-85) REVERT: B 12 GLU cc_start: 0.9300 (pt0) cc_final: 0.8966 (pm20) REVERT: B 36 ASN cc_start: 0.8593 (m-40) cc_final: 0.8214 (p0) REVERT: B 59 TYR cc_start: 0.8428 (m-80) cc_final: 0.7961 (m-80) REVERT: B 75 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8786 (mm-40) REVERT: B 283 ARG cc_start: 0.7608 (ttt180) cc_final: 0.7237 (ttt180) REVERT: B 292 PHE cc_start: 0.8130 (m-10) cc_final: 0.7715 (m-10) REVERT: G 21 MET cc_start: 0.8455 (mmm) cc_final: 0.7284 (mtm) REVERT: G 38 MET cc_start: 0.6677 (ptp) cc_final: 0.6277 (ptt) REVERT: G 42 GLU cc_start: 0.8047 (tp30) cc_final: 0.7541 (mt-10) REVERT: G 58 GLU cc_start: 0.9118 (mp0) cc_final: 0.8582 (mp0) REVERT: R 53 CYS cc_start: 0.9093 (m) cc_final: 0.8807 (p) REVERT: R 94 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7442 (t70) REVERT: R 109 GLU cc_start: 0.8721 (tp30) cc_final: 0.8268 (tm-30) REVERT: R 111 MET cc_start: 0.8559 (mtm) cc_final: 0.8205 (ptp) REVERT: R 446 HIS cc_start: 0.8961 (OUTLIER) cc_final: 0.8738 (t70) REVERT: H 148 ARG cc_start: 0.8845 (tpp-160) cc_final: 0.8464 (mmm160) REVERT: H 160 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8207 (p) REVERT: H 234 GLU cc_start: 0.6756 (pm20) cc_final: 0.6141 (pp20) outliers start: 32 outliers final: 17 residues processed: 199 average time/residue: 0.2293 time to fit residues: 61.6804 Evaluate side-chains 173 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 160 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8768 Z= 0.332 Angle : 0.837 13.750 11881 Z= 0.420 Chirality : 0.045 0.209 1349 Planarity : 0.005 0.077 1496 Dihedral : 7.867 153.449 1193 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.23 % Allowed : 23.01 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.40 (0.26), residues: 1075 helix: 1.26 (0.28), residues: 342 sheet: -0.25 (0.34), residues: 255 loop : -1.40 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.006 0.001 HIS B 225 PHE 0.032 0.002 PHE R 387 TYR 0.027 0.002 TYR A 320 ARG 0.006 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8320 (mm) REVERT: A 228 LEU cc_start: 0.3744 (OUTLIER) cc_final: 0.3419 (pp) REVERT: A 313 ARG cc_start: 0.8962 (mmm160) cc_final: 0.8748 (mmm-85) REVERT: B 12 GLU cc_start: 0.9279 (pt0) cc_final: 0.8949 (pm20) REVERT: B 36 ASN cc_start: 0.8586 (m-40) cc_final: 0.8272 (p0) REVERT: B 78 LYS cc_start: 0.9603 (mmmm) cc_final: 0.9153 (mmmm) REVERT: B 261 LEU cc_start: 0.9051 (mt) cc_final: 0.8844 (mp) REVERT: B 292 PHE cc_start: 0.8476 (m-10) cc_final: 0.8041 (m-80) REVERT: G 21 MET cc_start: 0.8465 (mmm) cc_final: 0.7315 (mtm) REVERT: G 38 MET cc_start: 0.6649 (ptp) cc_final: 0.6093 (ptt) REVERT: G 42 GLU cc_start: 0.8120 (tp30) cc_final: 0.7577 (mt-10) REVERT: G 58 GLU cc_start: 0.9173 (mp0) cc_final: 0.8483 (mp0) REVERT: R 53 CYS cc_start: 0.9109 (m) cc_final: 0.8835 (p) REVERT: R 94 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7537 (t70) REVERT: R 109 GLU cc_start: 0.8785 (tp30) cc_final: 0.8337 (tm-30) REVERT: R 446 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8781 (t70) REVERT: H 34 MET cc_start: 0.8660 (tpp) cc_final: 0.8299 (tpp) REVERT: H 160 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8204 (p) REVERT: H 218 MET cc_start: 0.8716 (tmm) cc_final: 0.8471 (ppp) outliers start: 30 outliers final: 21 residues processed: 170 average time/residue: 0.2173 time to fit residues: 50.7102 Evaluate side-chains 169 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 99 optimal weight: 40.0000 chunk 58 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.0270 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS R 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8768 Z= 0.230 Angle : 0.841 14.303 11881 Z= 0.411 Chirality : 0.045 0.200 1349 Planarity : 0.004 0.049 1496 Dihedral : 7.777 151.765 1193 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.90 % Allowed : 24.09 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.43 (0.26), residues: 1075 helix: 1.27 (0.29), residues: 336 sheet: -0.19 (0.34), residues: 248 loop : -1.45 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.010 0.001 HIS R 138 PHE 0.031 0.001 PHE R 387 TYR 0.024 0.001 TYR A 320 ARG 0.004 0.000 ARG R 450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8615 (tm-30) REVERT: A 228 LEU cc_start: 0.3663 (OUTLIER) cc_final: 0.3355 (pp) REVERT: A 313 ARG cc_start: 0.8916 (mmm160) cc_final: 0.8709 (mmm-85) REVERT: B 12 GLU cc_start: 0.9285 (pt0) cc_final: 0.8953 (pm20) REVERT: B 36 ASN cc_start: 0.8596 (m-40) cc_final: 0.8264 (p0) REVERT: B 78 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9210 (mmmm) REVERT: B 283 ARG cc_start: 0.7656 (ttt180) cc_final: 0.6960 (ttt90) REVERT: B 292 PHE cc_start: 0.8381 (m-10) cc_final: 0.7969 (m-80) REVERT: G 21 MET cc_start: 0.8467 (mmm) cc_final: 0.7324 (mtm) REVERT: G 38 MET cc_start: 0.6595 (ptp) cc_final: 0.6192 (ptt) REVERT: G 42 GLU cc_start: 0.8072 (tp30) cc_final: 0.7567 (mt-10) REVERT: G 58 GLU cc_start: 0.9157 (mp0) cc_final: 0.8616 (mp0) REVERT: R 53 CYS cc_start: 0.9099 (m) cc_final: 0.8796 (p) REVERT: R 94 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7514 (t70) REVERT: R 109 GLU cc_start: 0.8737 (tp30) cc_final: 0.8290 (tm-30) REVERT: H 34 MET cc_start: 0.8624 (tpp) cc_final: 0.8280 (tpp) REVERT: H 148 ARG cc_start: 0.8787 (tpp-160) cc_final: 0.8444 (mmm160) REVERT: H 218 MET cc_start: 0.8742 (tmm) cc_final: 0.8507 (ppp) outliers start: 27 outliers final: 21 residues processed: 179 average time/residue: 0.2359 time to fit residues: 57.1253 Evaluate side-chains 169 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain R residue 439 VAL Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 40.0000 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 176 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8768 Z= 0.288 Angle : 0.863 14.300 11881 Z= 0.427 Chirality : 0.046 0.205 1349 Planarity : 0.004 0.056 1496 Dihedral : 7.769 149.534 1193 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.58 % Allowed : 24.30 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.49 (0.26), residues: 1075 helix: 1.22 (0.29), residues: 336 sheet: -0.29 (0.33), residues: 253 loop : -1.45 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.011 0.001 HIS R 138 PHE 0.034 0.002 PHE R 387 TYR 0.021 0.002 TYR A 320 ARG 0.009 0.001 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8604 (tm-30) REVERT: A 36 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8298 (mm) REVERT: A 228 LEU cc_start: 0.3995 (OUTLIER) cc_final: 0.3720 (pp) REVERT: A 313 ARG cc_start: 0.8936 (mmm160) cc_final: 0.8724 (mmm-85) REVERT: B 12 GLU cc_start: 0.9283 (pt0) cc_final: 0.8951 (pm20) REVERT: B 36 ASN cc_start: 0.8589 (m-40) cc_final: 0.8275 (p0) REVERT: B 78 LYS cc_start: 0.9492 (mmmm) cc_final: 0.9230 (mmmm) REVERT: B 283 ARG cc_start: 0.7750 (ttt180) cc_final: 0.7014 (ttt90) REVERT: B 292 PHE cc_start: 0.8460 (m-10) cc_final: 0.8006 (m-80) REVERT: G 21 MET cc_start: 0.8472 (mmm) cc_final: 0.7365 (mtm) REVERT: G 38 MET cc_start: 0.6655 (ptp) cc_final: 0.6381 (ptt) REVERT: G 42 GLU cc_start: 0.8068 (tp30) cc_final: 0.7599 (mt-10) REVERT: G 58 GLU cc_start: 0.9179 (mp0) cc_final: 0.8497 (mp0) REVERT: R 53 CYS cc_start: 0.9103 (m) cc_final: 0.8809 (p) REVERT: R 94 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7587 (t70) REVERT: R 109 GLU cc_start: 0.8764 (tp30) cc_final: 0.8303 (tm-30) REVERT: H 34 MET cc_start: 0.8614 (tpp) cc_final: 0.8283 (tpp) REVERT: H 218 MET cc_start: 0.8728 (tmm) cc_final: 0.8507 (ppp) REVERT: H 234 GLU cc_start: 0.6832 (pm20) cc_final: 0.6064 (pp20) outliers start: 24 outliers final: 21 residues processed: 162 average time/residue: 0.2165 time to fit residues: 47.6950 Evaluate side-chains 166 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 401 CYS Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain R residue 439 VAL Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.093267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.069550 restraints weight = 31444.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071662 restraints weight = 17023.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072988 restraints weight = 11589.306| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8768 Z= 0.209 Angle : 0.840 15.220 11881 Z= 0.407 Chirality : 0.044 0.208 1349 Planarity : 0.004 0.051 1496 Dihedral : 7.585 145.963 1193 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.26 % Allowed : 24.62 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.38 (0.26), residues: 1075 helix: 1.26 (0.29), residues: 337 sheet: -0.16 (0.34), residues: 255 loop : -1.41 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS R 138 PHE 0.030 0.001 PHE R 387 TYR 0.015 0.001 TYR R 156 ARG 0.008 0.001 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1983.90 seconds wall clock time: 37 minutes 8.55 seconds (2228.55 seconds total)