Starting phenix.real_space_refine on Mon Mar 11 13:41:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/03_2024/8wc4_37430_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/03_2024/8wc4_37430.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/03_2024/8wc4_37430_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/03_2024/8wc4_37430_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/03_2024/8wc4_37430_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/03_2024/8wc4_37430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/03_2024/8wc4_37430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/03_2024/8wc4_37430_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc4_37430/03_2024/8wc4_37430_neut_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.079 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 Br 1 7.06 5 S 56 5.16 5 C 5369 2.51 5 N 1426 2.21 5 O 1542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 359": "OE1" <-> "OE2" Residue "R ARG 221": "NH1" <-> "NH2" Residue "R ARG 309": "NH1" <-> "NH2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8394 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1844 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2484 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2054 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "S" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1622 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 204} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "Y" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 380 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'VMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.77, per 1000 atoms: 0.57 Number of scatterers: 8394 At special positions: 0 Unit cell: (89.25, 118.15, 124.95, 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) Br 1 34.99 S 56 16.00 O 1542 8.00 N 1426 7.00 C 5369 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.5 seconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 34.4% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.191A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.539A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.529A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 301 through 318 removed outlier: 3.615A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 Processing helix chain 'B' and resid 7 through 25 removed outlier: 4.169A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.706A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 48 removed outlier: 3.721A pdb=" N ILE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE R 44 " --> pdb=" O ASN R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 84 removed outlier: 4.547A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 95 through 125 removed outlier: 3.731A pdb=" N ALA R 123 " --> pdb=" O ASP R 119 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 133 No H-bonds generated for 'chain 'R' and resid 130 through 133' Processing helix chain 'R' and resid 136 through 159 removed outlier: 3.969A pdb=" N LEU R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL R 141 " --> pdb=" O SER R 137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET R 142 " --> pdb=" O THR R 138 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 189 through 197 Processing helix chain 'R' and resid 199 through 225 removed outlier: 3.538A pdb=" N ILE R 223 " --> pdb=" O GLN R 219 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN R 224 " --> pdb=" O ALA R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 274 removed outlier: 3.587A pdb=" N THR R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) Proline residue: R 263 - end of helix Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 280 through 301 removed outlier: 3.773A pdb=" N ASP R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR R 291 " --> pdb=" O TYR R 287 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 306 through 312 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 30 through 47 removed outlier: 3.604A pdb=" N ASP Y 36 " --> pdb=" O LYS Y 32 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYS Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLU Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 253 through 259 removed outlier: 4.128A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN A 195 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU A 36 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU A 38 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N VAL A 201 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.899A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.902A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.634A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.997A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 250 through 254 removed outlier: 3.516A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.608A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.808A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.739A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 95 through 99 removed outlier: 3.525A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.566A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.839A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 174 through 176 354 hydrogen bonds defined for protein. 1029 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: 2.28 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 1357 1.31 - 1.47: 3583 1.47 - 1.63: 3558 1.63 - 1.78: 7 1.78 - 1.94: 75 Bond restraints: 8580 Sorted by residual: bond pdb=" C PRO R 56 " pdb=" O PRO R 56 " ideal model delta sigma weight residual 1.238 1.158 0.080 1.24e-02 6.50e+03 4.16e+01 bond pdb=" C MET R 195 " pdb=" O MET R 195 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.16e-02 7.43e+03 2.59e+01 bond pdb=" CA ASN A 231 " pdb=" C ASN A 231 " ideal model delta sigma weight residual 1.525 1.474 0.051 1.02e-02 9.61e+03 2.49e+01 bond pdb=" C ASP B 312 " pdb=" O ASP B 312 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.38e-02 5.25e+03 2.46e+01 bond pdb=" CA PHE R 50 " pdb=" C PHE R 50 " ideal model delta sigma weight residual 1.524 1.490 0.034 7.00e-03 2.04e+04 2.41e+01 ... (remaining 8575 not shown) Histogram of bond angle deviations from ideal: 97.01 - 104.87: 126 104.87 - 112.73: 4529 112.73 - 120.59: 3744 120.59 - 128.45: 3195 128.45 - 136.31: 72 Bond angle restraints: 11666 Sorted by residual: angle pdb=" N GLN R 52 " pdb=" CA GLN R 52 " pdb=" C GLN R 52 " ideal model delta sigma weight residual 112.45 97.01 15.44 1.39e+00 5.18e-01 1.23e+02 angle pdb=" C ILE R 223 " pdb=" CA ILE R 223 " pdb=" CB ILE R 223 " ideal model delta sigma weight residual 111.70 102.14 9.56 1.28e+00 6.10e-01 5.58e+01 angle pdb=" N ALA R 311 " pdb=" CA ALA R 311 " pdb=" C ALA R 311 " ideal model delta sigma weight residual 112.90 103.86 9.04 1.31e+00 5.83e-01 4.76e+01 angle pdb=" C THR R 55 " pdb=" N PRO R 56 " pdb=" CA PRO R 56 " ideal model delta sigma weight residual 119.28 126.65 -7.37 1.10e+00 8.26e-01 4.49e+01 angle pdb=" N TYR R 305 " pdb=" CA TYR R 305 " pdb=" C TYR R 305 " ideal model delta sigma weight residual 109.72 117.84 -8.12 1.25e+00 6.40e-01 4.22e+01 ... (remaining 11661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 4569 16.03 - 32.05: 349 32.05 - 48.08: 75 48.08 - 64.11: 12 64.11 - 80.13: 13 Dihedral angle restraints: 5018 sinusoidal: 1793 harmonic: 3225 Sorted by residual: dihedral pdb=" N LYS R 51 " pdb=" C LYS R 51 " pdb=" CA LYS R 51 " pdb=" CB LYS R 51 " ideal model delta harmonic sigma weight residual 122.80 139.77 -16.97 0 2.50e+00 1.60e-01 4.61e+01 dihedral pdb=" C LYS R 51 " pdb=" N LYS R 51 " pdb=" CA LYS R 51 " pdb=" CB LYS R 51 " ideal model delta harmonic sigma weight residual -122.60 -136.57 13.97 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C ILE R 45 " pdb=" N ILE R 45 " pdb=" CA ILE R 45 " pdb=" CB ILE R 45 " ideal model delta harmonic sigma weight residual -122.00 -134.17 12.17 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 5015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1293 0.120 - 0.239: 39 0.239 - 0.359: 5 0.359 - 0.478: 3 0.478 - 0.598: 1 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CA LYS R 51 " pdb=" N LYS R 51 " pdb=" C LYS R 51 " pdb=" CB LYS R 51 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" CA PHE R 50 " pdb=" N PHE R 50 " pdb=" C PHE R 50 " pdb=" CB PHE R 50 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILE R 45 " pdb=" CA ILE R 45 " pdb=" CG1 ILE R 45 " pdb=" CG2 ILE R 45 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1338 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP R 88 " 0.022 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C TRP R 88 " -0.079 2.00e-02 2.50e+03 pdb=" O TRP R 88 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR R 89 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 194 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C PHE R 194 " 0.071 2.00e-02 2.50e+03 pdb=" O PHE R 194 " -0.027 2.00e-02 2.50e+03 pdb=" N MET R 195 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 55 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C THR R 55 " -0.058 2.00e-02 2.50e+03 pdb=" O THR R 55 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO R 56 " 0.019 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1148 2.75 - 3.29: 7809 3.29 - 3.83: 12928 3.83 - 4.36: 14826 4.36 - 4.90: 27146 Nonbonded interactions: 63857 Sorted by model distance: nonbonded pdb=" ND2 ASN R 40 " pdb=" OD1 ASP R 68 " model vdw 2.216 2.520 nonbonded pdb=" O GLN S 39 " pdb=" OG1 THR S 116 " model vdw 2.237 2.440 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.325 2.440 nonbonded pdb=" NH1 ARG B 49 " pdb=" O TYR B 85 " model vdw 2.333 2.520 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.334 2.520 ... (remaining 63852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 4.060 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.280 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 0.080 8580 Z= 0.391 Angle : 0.808 15.445 11666 Z= 0.487 Chirality : 0.059 0.598 1341 Planarity : 0.005 0.047 1474 Dihedral : 12.939 80.132 2926 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.93 % Allowed : 1.28 % Favored : 97.79 % Cbeta Deviations : 0.19 % 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: -0.26 (0.26), residues: 1084 helix: 1.22 (0.27), residues: 377 sheet: 0.20 (0.33), residues: 256 loop : -1.62 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.012 0.002 HIS R 49 PHE 0.018 0.002 PHE R 214 TYR 0.030 0.002 TYR A 230 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 0.899 Fit side-chains REVERT: A 234 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7431 (tp-100) REVERT: A 238 ASN cc_start: 0.8730 (m110) cc_final: 0.8403 (m110) REVERT: A 323 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7818 (ttm110) REVERT: B 247 ASP cc_start: 0.7774 (t0) cc_final: 0.7573 (t0) REVERT: R 157 MET cc_start: 0.7804 (ttm) cc_final: 0.7443 (ttm) REVERT: R 224 ASN cc_start: 0.7546 (m-40) cc_final: 0.7288 (m110) REVERT: S 18 ARG cc_start: 0.8407 (tpp80) cc_final: 0.7818 (ttm170) outliers start: 8 outliers final: 5 residues processed: 167 average time/residue: 0.2312 time to fit residues: 50.9939 Evaluate side-chains 135 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 HIS Chi-restraints excluded: chain R residue 54 HIS Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 310 ARG Chi-restraints excluded: chain Y residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 204 GLN B 32 GLN R 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8580 Z= 0.175 Angle : 0.558 10.393 11666 Z= 0.290 Chirality : 0.042 0.140 1341 Planarity : 0.004 0.042 1474 Dihedral : 5.486 56.258 1202 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.17 % Allowed : 7.46 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1084 helix: 1.76 (0.27), residues: 377 sheet: 0.25 (0.33), residues: 247 loop : -1.45 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.006 0.001 HIS R 62 PHE 0.018 0.001 PHE A 189 TYR 0.039 0.002 TYR R 287 ARG 0.003 0.000 ARG Y 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 0.835 Fit side-chains REVERT: A 24 GLN cc_start: 0.7368 (tt0) cc_final: 0.7071 (mt0) REVERT: A 238 ASN cc_start: 0.8745 (m110) cc_final: 0.8488 (m110) REVERT: B 247 ASP cc_start: 0.7640 (t0) cc_final: 0.7401 (t0) REVERT: R 157 MET cc_start: 0.7774 (ttm) cc_final: 0.7402 (ttm) outliers start: 10 outliers final: 4 residues processed: 150 average time/residue: 0.2409 time to fit residues: 47.8573 Evaluate side-chains 137 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 HIS Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 261 GLN B 32 GLN B 268 ASN ** R 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8580 Z= 0.172 Angle : 0.521 9.715 11666 Z= 0.270 Chirality : 0.042 0.143 1341 Planarity : 0.004 0.042 1474 Dihedral : 4.536 43.987 1192 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.40 % Allowed : 11.42 % Favored : 87.18 % 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: 0.38 (0.26), residues: 1084 helix: 2.03 (0.27), residues: 376 sheet: 0.38 (0.32), residues: 272 loop : -1.47 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 PHE 0.013 0.001 PHE A 189 TYR 0.031 0.001 TYR R 287 ARG 0.005 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 0.970 Fit side-chains REVERT: A 24 GLN cc_start: 0.7410 (tt0) cc_final: 0.7106 (mt0) REVERT: A 238 ASN cc_start: 0.8780 (m110) cc_final: 0.8509 (m110) REVERT: R 54 HIS cc_start: 0.6767 (m170) cc_final: 0.6558 (m170) outliers start: 12 outliers final: 8 residues processed: 144 average time/residue: 0.2127 time to fit residues: 41.2246 Evaluate side-chains 136 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 100 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 0.3980 chunk 94 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 261 GLN B 32 GLN B 175 GLN ** R 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8580 Z= 0.140 Angle : 0.491 9.882 11666 Z= 0.254 Chirality : 0.041 0.133 1341 Planarity : 0.004 0.042 1474 Dihedral : 4.105 35.647 1190 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.28 % Allowed : 12.35 % Favored : 86.36 % 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: 0.52 (0.26), residues: 1084 helix: 2.18 (0.27), residues: 377 sheet: 0.45 (0.31), residues: 272 loop : -1.44 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.007 0.001 HIS R 62 PHE 0.013 0.001 PHE A 189 TYR 0.034 0.001 TYR R 287 ARG 0.007 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 0.951 Fit side-chains REVERT: A 24 GLN cc_start: 0.7383 (tt0) cc_final: 0.7062 (mt0) REVERT: A 238 ASN cc_start: 0.8775 (m110) cc_final: 0.8492 (m110) REVERT: B 59 TYR cc_start: 0.8488 (m-10) cc_final: 0.8214 (m-10) REVERT: R 54 HIS cc_start: 0.6678 (m170) cc_final: 0.6443 (m170) REVERT: R 170 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7957 (tt) REVERT: S 18 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.7746 (tpt90) outliers start: 11 outliers final: 5 residues processed: 142 average time/residue: 0.2136 time to fit residues: 40.9097 Evaluate side-chains 142 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 170 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.0270 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 190 GLN B 32 GLN B 175 GLN ** R 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8580 Z= 0.129 Angle : 0.482 9.499 11666 Z= 0.248 Chirality : 0.040 0.138 1341 Planarity : 0.003 0.044 1474 Dihedral : 3.933 30.298 1190 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.21 % Allowed : 12.35 % Favored : 85.43 % 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: 0.65 (0.26), residues: 1084 helix: 2.28 (0.27), residues: 377 sheet: 0.57 (0.32), residues: 271 loop : -1.37 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.007 0.001 HIS R 62 PHE 0.012 0.001 PHE A 189 TYR 0.016 0.001 TYR A 230 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 0.999 Fit side-chains REVERT: A 24 GLN cc_start: 0.7381 (tt0) cc_final: 0.7052 (mt0) REVERT: A 238 ASN cc_start: 0.8739 (m110) cc_final: 0.8474 (m110) REVERT: R 54 HIS cc_start: 0.6625 (m170) cc_final: 0.6409 (m170) REVERT: R 170 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7924 (tt) REVERT: S 18 ARG cc_start: 0.8304 (tpp-160) cc_final: 0.7743 (tpt90) REVERT: S 83 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.5748 (mmt) outliers start: 19 outliers final: 11 residues processed: 148 average time/residue: 0.2213 time to fit residues: 44.8920 Evaluate side-chains 146 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.3980 chunk 20 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 87 optimal weight: 0.0570 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 32 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8580 Z= 0.125 Angle : 0.471 8.321 11666 Z= 0.244 Chirality : 0.040 0.127 1341 Planarity : 0.003 0.045 1474 Dihedral : 3.819 26.958 1190 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.63 % Allowed : 13.17 % Favored : 85.20 % 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: 0.73 (0.26), residues: 1084 helix: 2.30 (0.27), residues: 378 sheet: 0.67 (0.32), residues: 266 loop : -1.32 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.007 0.001 HIS R 62 PHE 0.022 0.001 PHE R 207 TYR 0.027 0.001 TYR R 287 ARG 0.011 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 0.979 Fit side-chains REVERT: A 24 GLN cc_start: 0.7372 (tt0) cc_final: 0.7038 (mt0) REVERT: A 238 ASN cc_start: 0.8734 (m110) cc_final: 0.8466 (m110) REVERT: R 170 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7930 (tt) REVERT: S 18 ARG cc_start: 0.8298 (tpp-160) cc_final: 0.7701 (tpt170) REVERT: Y 62 ARG cc_start: 0.7641 (ptt-90) cc_final: 0.7440 (ptt-90) outliers start: 14 outliers final: 9 residues processed: 149 average time/residue: 0.2151 time to fit residues: 43.5558 Evaluate side-chains 144 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 296 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.0020 chunk 41 optimal weight: 0.7980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 32 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8580 Z= 0.149 Angle : 0.487 8.250 11666 Z= 0.253 Chirality : 0.041 0.134 1341 Planarity : 0.003 0.047 1474 Dihedral : 3.840 26.680 1190 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.52 % Allowed : 14.10 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1084 helix: 2.32 (0.27), residues: 377 sheet: 0.70 (0.32), residues: 256 loop : -1.36 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.007 0.001 HIS R 62 PHE 0.018 0.001 PHE R 207 TYR 0.024 0.001 TYR R 287 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.056 Fit side-chains REVERT: A 24 GLN cc_start: 0.7405 (tt0) cc_final: 0.7062 (mt0) REVERT: A 238 ASN cc_start: 0.8759 (m110) cc_final: 0.8475 (m110) REVERT: R 157 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7196 (ttm) REVERT: R 170 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7965 (tt) REVERT: S 18 ARG cc_start: 0.8271 (tpp-160) cc_final: 0.7722 (tpt170) REVERT: S 83 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.5835 (mmt) outliers start: 13 outliers final: 9 residues processed: 144 average time/residue: 0.2069 time to fit residues: 40.8670 Evaluate side-chains 145 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 157 MET Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 91 optimal weight: 0.0770 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 32 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8580 Z= 0.246 Angle : 0.555 9.968 11666 Z= 0.289 Chirality : 0.043 0.151 1341 Planarity : 0.004 0.047 1474 Dihedral : 4.245 32.051 1190 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.86 % Allowed : 14.69 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1084 helix: 2.22 (0.27), residues: 378 sheet: 0.61 (0.32), residues: 258 loop : -1.37 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.009 0.001 HIS R 62 PHE 0.018 0.002 PHE R 207 TYR 0.021 0.002 TYR R 287 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.011 Fit side-chains REVERT: A 24 GLN cc_start: 0.7503 (tt0) cc_final: 0.7194 (mt0) REVERT: A 234 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7639 (tp-100) REVERT: A 238 ASN cc_start: 0.8795 (m110) cc_final: 0.8517 (m110) REVERT: B 258 ASP cc_start: 0.7477 (t0) cc_final: 0.7269 (t0) REVERT: R 157 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7225 (ttm) REVERT: R 170 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8100 (tt) REVERT: S 18 ARG cc_start: 0.8301 (tpp-160) cc_final: 0.7717 (tpt170) REVERT: S 83 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6069 (mmt) outliers start: 16 outliers final: 11 residues processed: 140 average time/residue: 0.2083 time to fit residues: 40.0488 Evaluate side-chains 143 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 157 MET Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 32 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8580 Z= 0.211 Angle : 0.529 9.438 11666 Z= 0.275 Chirality : 0.042 0.143 1341 Planarity : 0.004 0.047 1474 Dihedral : 4.212 31.649 1190 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.75 % Allowed : 15.15 % Favored : 83.10 % 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: 0.59 (0.26), residues: 1084 helix: 2.19 (0.27), residues: 378 sheet: 0.60 (0.32), residues: 258 loop : -1.38 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.008 0.001 HIS R 62 PHE 0.017 0.001 PHE R 207 TYR 0.022 0.001 TYR R 287 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.933 Fit side-chains REVERT: A 24 GLN cc_start: 0.7498 (tt0) cc_final: 0.7169 (mt0) REVERT: A 238 ASN cc_start: 0.8793 (m110) cc_final: 0.8506 (m110) REVERT: B 258 ASP cc_start: 0.7506 (t0) cc_final: 0.7284 (t0) REVERT: R 68 ASP cc_start: 0.7102 (t70) cc_final: 0.6444 (t70) REVERT: R 157 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7183 (ttm) REVERT: R 170 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8072 (tt) REVERT: S 18 ARG cc_start: 0.8281 (tpp-160) cc_final: 0.7712 (tpt170) REVERT: S 83 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6105 (mmt) outliers start: 15 outliers final: 11 residues processed: 138 average time/residue: 0.2261 time to fit residues: 42.1322 Evaluate side-chains 141 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 157 MET Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 294 SER Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 7.9990 chunk 71 optimal weight: 0.0000 chunk 108 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 32 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8580 Z= 0.205 Angle : 0.533 9.073 11666 Z= 0.278 Chirality : 0.042 0.145 1341 Planarity : 0.004 0.046 1474 Dihedral : 4.211 31.573 1190 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.86 % Allowed : 15.73 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1084 helix: 2.17 (0.27), residues: 378 sheet: 0.59 (0.32), residues: 258 loop : -1.38 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 59 HIS 0.008 0.001 HIS R 62 PHE 0.017 0.001 PHE R 207 TYR 0.032 0.001 TYR R 287 ARG 0.004 0.000 ARG B 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.996 Fit side-chains REVERT: A 24 GLN cc_start: 0.7510 (tt0) cc_final: 0.7178 (mt0) REVERT: A 238 ASN cc_start: 0.8790 (m110) cc_final: 0.8508 (m110) REVERT: B 258 ASP cc_start: 0.7521 (t0) cc_final: 0.7284 (t0) REVERT: R 68 ASP cc_start: 0.7090 (t70) cc_final: 0.6426 (t70) REVERT: R 157 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7192 (ttm) REVERT: R 170 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8075 (tt) REVERT: S 18 ARG cc_start: 0.8284 (tpp-160) cc_final: 0.7734 (tpt170) REVERT: S 83 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6116 (mmt) outliers start: 16 outliers final: 10 residues processed: 138 average time/residue: 0.2175 time to fit residues: 40.9545 Evaluate side-chains 139 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 HIS Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 157 MET Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 294 SER Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 86 optimal weight: 0.0370 chunk 36 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 32 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.148625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114777 restraints weight = 10636.753| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.37 r_work: 0.3161 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8580 Z= 0.178 Angle : 0.512 8.348 11666 Z= 0.267 Chirality : 0.041 0.139 1341 Planarity : 0.003 0.046 1474 Dihedral : 4.125 30.945 1190 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.63 % Allowed : 15.85 % Favored : 82.52 % 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: 0.61 (0.26), residues: 1084 helix: 2.21 (0.27), residues: 378 sheet: 0.54 (0.32), residues: 260 loop : -1.34 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 59 HIS 0.008 0.001 HIS R 62 PHE 0.016 0.001 PHE R 207 TYR 0.029 0.001 TYR R 287 ARG 0.004 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.88 seconds wall clock time: 40 minutes 44.24 seconds (2444.24 seconds total)