Starting phenix.real_space_refine on Wed Feb 14 01:21:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/02_2024/8hdp_34677_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/02_2024/8hdp_34677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/02_2024/8hdp_34677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/02_2024/8hdp_34677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/02_2024/8hdp_34677_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdp_34677/02_2024/8hdp_34677_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 53 5.16 5 C 5280 2.51 5 N 1430 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8282 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1985 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2297 Unusual residues: {'ADN%rna3p': 1, 'CLR': 4} Classifications: {'peptide': 280, 'undetermined': 5} Modifications used: {'rna3p': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 268, None: 5} Not linked: pdbres="LEU R 309 " pdbres="ADN R 401 " Not linked: pdbres="ADN R 401 " pdbres="CLR R 402 " Not linked: pdbres="CLR R 402 " pdbres="CLR R 403 " Not linked: pdbres="CLR R 403 " pdbres="CLR R 404 " Not linked: pdbres="CLR R 404 " pdbres="CLR R 405 " Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.03, per 1000 atoms: 0.61 Number of scatterers: 8282 At special positions: 0 Unit cell: (95.68, 76.96, 130, 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 53 16.00 O 1519 8.00 N 1430 7.00 C 5280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.6 seconds 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 38.2% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 4.267A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.636A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 184 through 202 Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.218A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 7 through 34 Processing helix chain 'R' and resid 41 through 68 removed outlier: 4.397A pdb=" N ILE R 61 " --> pdb=" O GLY R 57 " (cutoff:3.500A) Proline residue: R 62 - end of helix Processing helix chain 'R' and resid 75 through 108 removed outlier: 3.583A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 116 No H-bonds generated for 'chain 'R' and resid 113 through 116' Processing helix chain 'R' and resid 119 through 137 Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 179 through 183 Processing helix chain 'R' and resid 187 through 190 No H-bonds generated for 'chain 'R' and resid 187 through 190' Processing helix chain 'R' and resid 192 through 213 Processing helix chain 'R' and resid 225 through 259 removed outlier: 3.572A pdb=" N PHE R 243 " --> pdb=" O ILE R 239 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 268 through 290 removed outlier: 4.472A pdb=" N ASN R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER R 283 " --> pdb=" O SER R 279 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 295 through 308 Processing sheet with id= A, first strand: chain 'A' and resid 139 through 142 removed outlier: 6.343A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN A 80 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU A 43 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS A 82 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU A 45 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE A 84 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLY A 47 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.965A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.503A 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 103 removed outlier: 6.891A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 150 removed outlier: 7.114A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.055A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.427A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.748A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.113A 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: 7.274A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.784A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1125 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: 2.50 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1448 1.33 - 1.45: 2236 1.45 - 1.57: 4701 1.57 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8458 Sorted by residual: bond pdb=" C4 ADN R 401 " pdb=" C5 ADN R 401 " ideal model delta sigma weight residual 1.385 1.467 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C5 ADN R 401 " pdb=" C6 ADN R 401 " ideal model delta sigma weight residual 1.408 1.482 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C MET R 238 " pdb=" O MET R 238 " ideal model delta sigma weight residual 1.236 1.202 0.033 1.17e-02 7.31e+03 8.14e+00 bond pdb=" N TRP R 247 " pdb=" CA TRP R 247 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.84e+00 bond pdb=" N GLU R 174 " pdb=" CA GLU R 174 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.27e-02 6.20e+03 6.58e+00 ... (remaining 8453 not shown) Histogram of bond angle deviations from ideal: 79.54 - 90.96: 3 90.96 - 102.38: 24 102.38 - 113.81: 4942 113.81 - 125.23: 6406 125.23 - 136.65: 123 Bond angle restraints: 11498 Sorted by residual: angle pdb=" C17 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sigma weight residual 110.18 79.54 30.64 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C12 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sigma weight residual 111.01 81.73 29.28 3.00e+00 1.11e-01 9.52e+01 angle pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sigma weight residual 112.24 90.75 21.49 3.00e+00 1.11e-01 5.13e+01 angle pdb=" C12 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C17 CLR R 404 " ideal model delta sigma weight residual 116.52 130.09 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C1' ADN R 401 " pdb=" C2' ADN R 401 " pdb=" C3' ADN R 401 " ideal model delta sigma weight residual 101.30 105.27 -3.97 1.00e+00 1.00e+00 1.58e+01 ... (remaining 11493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.51: 5158 34.51 - 69.01: 71 69.01 - 103.52: 5 103.52 - 138.02: 1 138.02 - 172.53: 5 Dihedral angle restraints: 5240 sinusoidal: 2209 harmonic: 3031 Sorted by residual: dihedral pdb=" C16 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C17 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sinusoidal sigma weight residual -78.02 94.51 -172.53 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C18 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C17 CLR R 404 " pdb=" C20 CLR R 404 " ideal model delta sinusoidal sigma weight residual 312.73 144.58 168.15 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C15 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sinusoidal sigma weight residual 69.18 -96.05 165.23 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 5237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.383: 1317 0.383 - 0.766: 1 0.766 - 1.149: 0 1.149 - 1.532: 0 1.532 - 1.914: 2 Chirality restraints: 1320 Sorted by residual: chirality pdb=" C13 CLR R 404 " pdb=" C12 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C17 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.93 -1.02 -1.91 2.00e-01 2.50e+01 9.16e+01 chirality pdb=" CG LEU R 3 " pdb=" CB LEU R 3 " pdb=" CD1 LEU R 3 " pdb=" CD2 LEU R 3 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.20e+01 chirality pdb=" CA GLN R 6 " pdb=" N GLN R 6 " pdb=" C GLN R 6 " pdb=" CB GLN R 6 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 1317 not shown) Planarity restraints: 1446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 237 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C ALA R 237 " 0.047 2.00e-02 2.50e+03 pdb=" O ALA R 237 " -0.018 2.00e-02 2.50e+03 pdb=" N MET R 238 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 173 " 0.010 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C PHE R 173 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE R 173 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU R 174 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 178 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C PRO R 178 " -0.036 2.00e-02 2.50e+03 pdb=" O PRO R 178 " 0.014 2.00e-02 2.50e+03 pdb=" N MET R 179 " 0.012 2.00e-02 2.50e+03 ... (remaining 1443 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 112 2.58 - 3.16: 7495 3.16 - 3.74: 13158 3.74 - 4.32: 18617 4.32 - 4.90: 30739 Nonbonded interactions: 70121 Sorted by model distance: nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.006 2.440 nonbonded pdb=" OG SER R 235 " pdb=" NH2 ARG R 293 " model vdw 2.022 2.520 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.080 2.520 nonbonded pdb=" OD1 ASP A 111 " pdb=" OG SER A 113 " model vdw 2.114 2.440 nonbonded pdb=" OG1 THR R 40 " pdb=" OD1 ASN R 43 " model vdw 2.136 2.440 ... (remaining 70116 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: 0.400 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: 0.000 Extract box with map and model: 2.190 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.450 Find NCS groups from input model: 0.210 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8458 Z= 0.221 Angle : 0.755 30.642 11498 Z= 0.343 Chirality : 0.085 1.914 1320 Planarity : 0.003 0.041 1446 Dihedral : 12.508 172.528 3271 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.57 % Allowed : 6.04 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.25), residues: 1027 helix: 0.17 (0.25), residues: 401 sheet: -2.09 (0.31), residues: 207 loop : -1.98 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 247 HIS 0.005 0.001 HIS R 251 PHE 0.014 0.001 PHE R 173 TYR 0.005 0.001 TYR R 10 ARG 0.002 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 289 time to evaluate : 1.014 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: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8121 (tt) cc_final: 0.7907 (pt) REVERT: A 212 TYR cc_start: 0.8614 (m-80) cc_final: 0.7915 (m-80) REVERT: B 9 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8586 (pp30) REVERT: B 10 GLU cc_start: 0.8695 (tp30) cc_final: 0.8409 (tp30) REVERT: B 63 TRP cc_start: 0.8484 (m100) cc_final: 0.8248 (m100) REVERT: B 171 ILE cc_start: 0.6986 (mp) cc_final: 0.6614 (mm) REVERT: B 280 LYS cc_start: 0.8845 (tttm) cc_final: 0.8560 (ttpp) REVERT: B 289 TYR cc_start: 0.8423 (m-80) cc_final: 0.7748 (m-80) REVERT: B 297 TRP cc_start: 0.7497 (m100) cc_final: 0.7256 (m100) REVERT: N 60 TYR cc_start: 0.8323 (m-80) cc_final: 0.7396 (m-80) REVERT: N 87 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8048 (mtmm) REVERT: R 227 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7691 (pt0) outliers start: 5 outliers final: 1 residues processed: 293 average time/residue: 0.2493 time to fit residues: 94.0153 Evaluate side-chains 179 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 239 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.0010 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN A 123 ASN B 62 HIS B 91 HIS B 119 ASN B 156 GLN B 230 ASN B 293 ASN B 295 ASN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN R 280 HIS ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8458 Z= 0.236 Angle : 0.758 31.198 11498 Z= 0.335 Chirality : 0.067 1.880 1320 Planarity : 0.004 0.055 1446 Dihedral : 11.976 168.201 1421 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.31 % Allowed : 12.09 % Favored : 84.61 % 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: -0.46 (0.26), residues: 1027 helix: 1.02 (0.26), residues: 406 sheet: -1.39 (0.33), residues: 204 loop : -0.97 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.018 0.001 PHE R 173 TYR 0.011 0.001 TYR B 59 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.002 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: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8626 (pp30) REVERT: B 10 GLU cc_start: 0.8730 (tp30) cc_final: 0.8415 (tp30) REVERT: B 15 LYS cc_start: 0.9224 (ptpt) cc_final: 0.8942 (ptpp) REVERT: G 22 GLU cc_start: 0.8982 (tp30) cc_final: 0.8534 (tp30) REVERT: N 32 TYR cc_start: 0.8435 (m-80) cc_final: 0.8004 (m-80) REVERT: N 51 ILE cc_start: 0.8526 (tt) cc_final: 0.8279 (pt) REVERT: N 53 GLN cc_start: 0.8329 (mp10) cc_final: 0.8107 (mp10) REVERT: N 60 TYR cc_start: 0.8361 (m-80) cc_final: 0.7503 (m-80) REVERT: N 65 LYS cc_start: 0.8803 (tptm) cc_final: 0.8559 (tppp) REVERT: N 80 TYR cc_start: 0.7938 (m-80) cc_final: 0.7704 (m-80) REVERT: R 7 ASP cc_start: 0.8438 (m-30) cc_final: 0.7751 (p0) REVERT: R 227 GLN cc_start: 0.8220 (mm-40) cc_final: 0.8012 (pt0) REVERT: R 229 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7208 (tm-30) outliers start: 29 outliers final: 18 residues processed: 189 average time/residue: 0.2524 time to fit residues: 62.1058 Evaluate side-chains 162 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 76 optimal weight: 0.0770 chunk 62 optimal weight: 50.0000 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS N 31 ASN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8458 Z= 0.165 Angle : 0.718 30.605 11498 Z= 0.312 Chirality : 0.065 1.870 1320 Planarity : 0.003 0.053 1446 Dihedral : 11.508 168.654 1419 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.85 % Allowed : 13.68 % Favored : 83.47 % 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: 0.00 (0.26), residues: 1027 helix: 1.40 (0.26), residues: 398 sheet: -1.06 (0.32), residues: 212 loop : -0.69 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.020 0.001 PHE B 199 TYR 0.013 0.001 TYR N 115 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8605 (pp30) REVERT: B 10 GLU cc_start: 0.8703 (tp30) cc_final: 0.8380 (tp30) REVERT: B 15 LYS cc_start: 0.9191 (ptpt) cc_final: 0.8956 (ptpp) REVERT: B 280 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8298 (ttmm) REVERT: G 22 GLU cc_start: 0.9087 (tp30) cc_final: 0.8452 (tp30) REVERT: N 32 TYR cc_start: 0.8550 (m-80) cc_final: 0.8070 (m-80) REVERT: N 53 GLN cc_start: 0.8397 (mp10) cc_final: 0.8185 (mp10) REVERT: N 60 TYR cc_start: 0.8278 (m-80) cc_final: 0.7272 (m-80) REVERT: N 80 TYR cc_start: 0.7947 (m-80) cc_final: 0.7582 (m-80) REVERT: R 7 ASP cc_start: 0.8400 (m-30) cc_final: 0.7661 (p0) REVERT: R 195 LEU cc_start: 0.8707 (tp) cc_final: 0.8506 (tp) REVERT: R 227 GLN cc_start: 0.8297 (mm-40) cc_final: 0.8025 (pt0) outliers start: 25 outliers final: 18 residues processed: 173 average time/residue: 0.2640 time to fit residues: 58.9902 Evaluate side-chains 157 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN N 31 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8458 Z= 0.287 Angle : 0.760 31.350 11498 Z= 0.339 Chirality : 0.066 1.844 1320 Planarity : 0.004 0.054 1446 Dihedral : 11.431 167.740 1419 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.65 % Allowed : 14.14 % Favored : 82.21 % 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: 0.19 (0.26), residues: 1027 helix: 1.45 (0.26), residues: 395 sheet: -0.96 (0.33), residues: 213 loop : -0.46 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.015 0.001 PHE B 199 TYR 0.015 0.001 TYR R 308 ARG 0.005 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8099 (tt) cc_final: 0.7739 (pt) REVERT: B 9 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8646 (pp30) REVERT: B 10 GLU cc_start: 0.8784 (tp30) cc_final: 0.8408 (tp30) REVERT: B 262 MET cc_start: 0.6881 (tpp) cc_final: 0.6664 (mmm) REVERT: B 280 LYS cc_start: 0.9054 (ttpp) cc_final: 0.8349 (ttmm) REVERT: G 22 GLU cc_start: 0.9094 (tp30) cc_final: 0.8869 (tp30) REVERT: N 60 TYR cc_start: 0.8331 (m-80) cc_final: 0.7184 (m-80) REVERT: N 82 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7954 (tp-100) REVERT: R 177 VAL cc_start: 0.8639 (t) cc_final: 0.8315 (m) REVERT: R 227 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8056 (pt0) REVERT: R 229 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7137 (tm-30) outliers start: 32 outliers final: 25 residues processed: 174 average time/residue: 0.2694 time to fit residues: 60.8710 Evaluate side-chains 165 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 0.0870 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8458 Z= 0.188 Angle : 0.729 30.807 11498 Z= 0.318 Chirality : 0.064 1.824 1320 Planarity : 0.003 0.056 1446 Dihedral : 11.299 170.335 1419 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.08 % Allowed : 15.39 % Favored : 81.53 % 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: 0.41 (0.27), residues: 1027 helix: 1.60 (0.26), residues: 399 sheet: -0.62 (0.33), residues: 208 loop : -0.45 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.016 0.001 PHE B 199 TYR 0.012 0.001 TYR A 170 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8073 (tt) cc_final: 0.7744 (pt) REVERT: B 9 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8655 (pp30) REVERT: B 10 GLU cc_start: 0.8791 (tp30) cc_final: 0.8420 (tp30) REVERT: B 261 LEU cc_start: 0.8549 (pp) cc_final: 0.8093 (pp) REVERT: B 280 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8393 (ttmm) REVERT: B 297 TRP cc_start: 0.8406 (m100) cc_final: 0.7958 (m100) REVERT: G 22 GLU cc_start: 0.9083 (tp30) cc_final: 0.8806 (tp30) REVERT: N 5 GLN cc_start: 0.7902 (mp10) cc_final: 0.7577 (mp10) REVERT: N 51 ILE cc_start: 0.8575 (tt) cc_final: 0.8236 (pt) REVERT: N 53 GLN cc_start: 0.8621 (mp10) cc_final: 0.8130 (mp10) REVERT: N 60 TYR cc_start: 0.8293 (m-80) cc_final: 0.7211 (m-80) REVERT: R 229 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7251 (tm-30) outliers start: 27 outliers final: 22 residues processed: 169 average time/residue: 0.2566 time to fit residues: 56.4738 Evaluate side-chains 160 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 57 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8458 Z= 0.259 Angle : 0.746 30.963 11498 Z= 0.330 Chirality : 0.064 1.816 1320 Planarity : 0.004 0.055 1446 Dihedral : 11.361 170.514 1419 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.65 % Allowed : 16.42 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1027 helix: 1.51 (0.26), residues: 399 sheet: -0.53 (0.34), residues: 204 loop : -0.41 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.015 0.001 PHE A 74 TYR 0.010 0.001 TYR N 95 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8182 (tt) cc_final: 0.7796 (pt) REVERT: B 9 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8705 (pp30) REVERT: B 10 GLU cc_start: 0.8814 (tp30) cc_final: 0.8434 (tp30) REVERT: B 280 LYS cc_start: 0.9079 (ttpp) cc_final: 0.8376 (ttmm) REVERT: G 29 LYS cc_start: 0.8935 (tppt) cc_final: 0.8677 (tppt) REVERT: N 53 GLN cc_start: 0.8610 (mp10) cc_final: 0.8116 (mp10) REVERT: N 60 TYR cc_start: 0.8302 (m-80) cc_final: 0.7222 (m-80) REVERT: N 80 TYR cc_start: 0.8144 (m-80) cc_final: 0.7900 (m-80) REVERT: N 105 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7798 (ptm160) REVERT: R 177 VAL cc_start: 0.8886 (t) cc_final: 0.8537 (m) REVERT: R 229 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7059 (tm-30) outliers start: 32 outliers final: 25 residues processed: 163 average time/residue: 0.2574 time to fit residues: 54.7158 Evaluate side-chains 162 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8458 Z= 0.224 Angle : 0.731 30.786 11498 Z= 0.321 Chirality : 0.064 1.812 1320 Planarity : 0.003 0.055 1446 Dihedral : 11.329 171.521 1419 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.53 % Allowed : 17.33 % Favored : 79.13 % 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: 0.48 (0.26), residues: 1027 helix: 1.58 (0.26), residues: 399 sheet: -0.47 (0.34), residues: 204 loop : -0.40 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.021 0.001 PHE R 187 TYR 0.012 0.001 TYR A 170 ARG 0.008 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 0.967 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: symmetry clash REVERT: A 62 ILE cc_start: 0.8200 (tt) cc_final: 0.7828 (pt) REVERT: B 9 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8716 (pp30) REVERT: B 10 GLU cc_start: 0.8854 (tp30) cc_final: 0.8480 (tp30) REVERT: B 280 LYS cc_start: 0.9080 (ttpp) cc_final: 0.8367 (ttmm) REVERT: G 29 LYS cc_start: 0.8960 (tppt) cc_final: 0.8630 (tppt) REVERT: N 5 GLN cc_start: 0.7978 (mp10) cc_final: 0.7631 (mp10) REVERT: N 60 TYR cc_start: 0.8262 (m-80) cc_final: 0.7162 (m-80) REVERT: N 73 ASP cc_start: 0.8329 (m-30) cc_final: 0.8041 (p0) REVERT: N 80 TYR cc_start: 0.8166 (m-80) cc_final: 0.7919 (m-80) REVERT: R 229 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7097 (tm-30) outliers start: 31 outliers final: 27 residues processed: 161 average time/residue: 0.2486 time to fit residues: 52.2297 Evaluate side-chains 166 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 0.0270 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8458 Z= 0.202 Angle : 0.734 30.669 11498 Z= 0.321 Chirality : 0.064 1.811 1320 Planarity : 0.004 0.055 1446 Dihedral : 11.301 172.343 1419 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.42 % Allowed : 18.13 % Favored : 78.45 % 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: 0.59 (0.26), residues: 1027 helix: 1.65 (0.26), residues: 399 sheet: -0.37 (0.34), residues: 204 loop : -0.34 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.020 0.001 PHE R 187 TYR 0.009 0.001 TYR N 95 ARG 0.008 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.023 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: symmetry clash REVERT: A 62 ILE cc_start: 0.8217 (tt) cc_final: 0.7928 (pt) REVERT: B 9 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8713 (pp30) REVERT: B 10 GLU cc_start: 0.8819 (tp30) cc_final: 0.8434 (tp30) REVERT: B 280 LYS cc_start: 0.9103 (ttpp) cc_final: 0.8398 (ttmm) REVERT: G 29 LYS cc_start: 0.8930 (tppt) cc_final: 0.8614 (tppt) REVERT: N 5 GLN cc_start: 0.8005 (mp10) cc_final: 0.7667 (mp10) REVERT: N 19 ARG cc_start: 0.8450 (ttt90) cc_final: 0.8162 (ttt90) REVERT: N 60 TYR cc_start: 0.8366 (m-80) cc_final: 0.7283 (m-80) REVERT: N 80 TYR cc_start: 0.8074 (m-80) cc_final: 0.7662 (m-80) REVERT: N 122 THR cc_start: 0.8516 (m) cc_final: 0.7991 (p) REVERT: R 229 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6944 (tm-30) outliers start: 30 outliers final: 26 residues processed: 165 average time/residue: 0.2499 time to fit residues: 54.7215 Evaluate side-chains 165 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8458 Z= 0.166 Angle : 0.721 30.581 11498 Z= 0.315 Chirality : 0.064 1.812 1320 Planarity : 0.003 0.055 1446 Dihedral : 11.243 172.621 1419 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.19 % Allowed : 18.36 % Favored : 78.45 % 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: 0.76 (0.27), residues: 1027 helix: 1.79 (0.26), residues: 398 sheet: -0.20 (0.35), residues: 202 loop : -0.29 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS A 209 PHE 0.015 0.001 PHE R 187 TYR 0.009 0.001 TYR N 95 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.039 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 62 ILE cc_start: 0.8259 (tt) cc_final: 0.7879 (pt) REVERT: B 9 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8719 (pp30) REVERT: B 10 GLU cc_start: 0.8812 (tp30) cc_final: 0.8422 (tp30) REVERT: B 280 LYS cc_start: 0.9095 (ttpp) cc_final: 0.8395 (ttmm) REVERT: G 29 LYS cc_start: 0.8962 (tppt) cc_final: 0.8644 (tppt) REVERT: N 5 GLN cc_start: 0.8067 (mp10) cc_final: 0.7710 (mp10) REVERT: N 19 ARG cc_start: 0.8501 (ttt90) cc_final: 0.8211 (ttt90) REVERT: N 60 TYR cc_start: 0.8503 (m-80) cc_final: 0.7465 (m-80) REVERT: N 80 TYR cc_start: 0.7998 (m-80) cc_final: 0.7355 (m-80) REVERT: R 229 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7097 (tm-30) outliers start: 28 outliers final: 25 residues processed: 162 average time/residue: 0.2396 time to fit residues: 51.2921 Evaluate side-chains 163 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8458 Z= 0.320 Angle : 0.779 30.637 11498 Z= 0.351 Chirality : 0.065 1.798 1320 Planarity : 0.004 0.072 1446 Dihedral : 11.437 173.222 1419 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.31 % Allowed : 18.59 % Favored : 78.11 % 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: 0.54 (0.26), residues: 1027 helix: 1.56 (0.26), residues: 399 sheet: -0.34 (0.34), residues: 200 loop : -0.36 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.024 0.001 PHE R 187 TYR 0.028 0.002 TYR N 115 ARG 0.012 0.001 ARG G 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8359 (tt) cc_final: 0.7951 (pt) REVERT: B 9 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8712 (pp30) REVERT: B 10 GLU cc_start: 0.8875 (tp30) cc_final: 0.8520 (tp30) REVERT: B 280 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8400 (ttmm) REVERT: G 29 LYS cc_start: 0.8911 (tppt) cc_final: 0.8573 (tppt) REVERT: N 5 GLN cc_start: 0.8037 (mp10) cc_final: 0.7750 (mp10) REVERT: N 19 ARG cc_start: 0.8545 (ttt90) cc_final: 0.8270 (ttt90) REVERT: N 31 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8199 (p0) REVERT: N 51 ILE cc_start: 0.8050 (pt) cc_final: 0.7717 (pt) REVERT: N 60 TYR cc_start: 0.8545 (m-80) cc_final: 0.7515 (m-80) REVERT: N 80 TYR cc_start: 0.8063 (m-80) cc_final: 0.7615 (m-80) REVERT: N 122 THR cc_start: 0.8527 (m) cc_final: 0.8158 (p) outliers start: 29 outliers final: 25 residues processed: 157 average time/residue: 0.2440 time to fit residues: 50.7160 Evaluate side-chains 159 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.102385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.077479 restraints weight = 16384.343| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.95 r_work: 0.3105 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8458 Z= 0.174 Angle : 0.730 30.505 11498 Z= 0.321 Chirality : 0.064 1.808 1320 Planarity : 0.003 0.055 1446 Dihedral : 11.325 173.629 1419 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.74 % Allowed : 19.95 % Favored : 77.31 % 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 (0.27), residues: 1027 helix: 1.71 (0.26), residues: 399 sheet: -0.28 (0.34), residues: 207 loop : -0.25 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 297 HIS 0.003 0.001 HIS A 209 PHE 0.016 0.001 PHE B 199 TYR 0.024 0.001 TYR N 115 ARG 0.006 0.000 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2088.16 seconds wall clock time: 38 minutes 45.30 seconds (2325.30 seconds total)