Starting phenix.real_space_refine on Wed Feb 12 23:40:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hdp_34677/02_2025/8hdp_34677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hdp_34677/02_2025/8hdp_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/cci-nas-00/data/ceres_data/8hdp_34677/02_2025/8hdp_34677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hdp_34677/02_2025/8hdp_34677.map" model { file = "/net/cci-nas-00/data/ceres_data/8hdp_34677/02_2025/8hdp_34677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hdp_34677/02_2025/8hdp_34677.cif" } 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. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8282 Number of models: 1 Model: "" Number of chains: 6 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: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2166 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 268} 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 Chain: "R" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {'ADN%rna3p': 1, 'CLR': 4} Classifications: {'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 4.85, per 1000 atoms: 0.59 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 984.4 milliseconds 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... Secondary structure from input PDB file: 28 helices and 10 sheets defined 42.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 9 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 52 through 56 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 114 through 130 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 145 through 156 removed outlier: 3.511A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.243A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.537A pdb=" N TYR A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.556A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.777A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.702A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.825A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 35 Processing helix chain 'R' and resid 40 through 59 Processing helix chain 'R' and resid 59 through 69 Processing helix chain 'R' and resid 74 through 109 removed outlier: 3.583A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 117 Processing helix chain 'R' and resid 118 through 138 Processing helix chain 'R' and resid 138 through 144 removed outlier: 3.814A pdb=" N LEU R 142 " --> pdb=" O LEU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 184 Processing helix chain 'R' and resid 186 through 191 Processing helix chain 'R' and resid 191 through 214 Processing helix chain 'R' and resid 225 through 260 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 267 through 291 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 294 through 309 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.317A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N ALA A 105 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG A 42 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE A 107 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 44 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL A 109 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 46 " --> pdb=" O VAL A 109 " (cutoff:3.500A) 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) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.605A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, 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: 6.125A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 5.651A pdb=" N CYS B 149 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER B 160 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE B 151 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 158 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.613A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (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=AA7, first strand: chain 'B' and resid 229 through 234 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=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.625A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (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=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, 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) 436 hydrogen bonds defined for protein. 1236 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: 2.55 Time building geometry restraints manager: 2.68 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: 0.00 - 6.13: 11482 6.13 - 12.26: 12 12.26 - 18.38: 1 18.38 - 24.51: 1 24.51 - 30.64: 2 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: 108 2.58 - 3.16: 7464 3.16 - 3.74: 13104 3.74 - 4.32: 18541 4.32 - 4.90: 30724 Nonbonded interactions: 69941 Sorted by model distance: nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.006 3.040 nonbonded pdb=" OG SER R 235 " pdb=" NH2 ARG R 293 " model vdw 2.022 3.120 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.080 3.120 nonbonded pdb=" OD1 ASP A 111 " pdb=" OG SER A 113 " model vdw 2.114 3.040 nonbonded pdb=" OG1 THR R 40 " pdb=" OD1 ASN R 43 " model vdw 2.136 3.040 ... (remaining 69936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.550 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.900 Find NCS groups from input model: 0.090 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.330 ------------------------------------------------------------------------------- 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= 0.211 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 to be fit. rotamer outliers: 5 poor density : 289 time to evaluate : 0.964 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: 0.2481 time to fit residues: 93.6897 Evaluate side-chains 179 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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: 1.9990 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN 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 295 ASN R 175 ASN R 280 HIS ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.109142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.084652 restraints weight = 16784.299| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.17 r_work: 0.3269 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8458 Z= 0.223 Angle : 0.766 30.957 11498 Z= 0.342 Chirality : 0.067 1.897 1320 Planarity : 0.004 0.057 1446 Dihedral : 11.972 166.520 1421 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.85 % Allowed : 12.31 % Favored : 84.83 % 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: -0.55 (0.26), residues: 1027 helix: 1.15 (0.26), residues: 392 sheet: -1.46 (0.31), residues: 214 loop : -1.15 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS A 209 PHE 0.019 0.001 PHE R 173 TYR 0.010 0.001 TYR N 95 ARG 0.005 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 203 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.893 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 230 ASP cc_start: 0.8348 (m-30) cc_final: 0.8100 (m-30) REVERT: B 9 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8826 (pp30) REVERT: B 10 GLU cc_start: 0.8908 (tp30) cc_final: 0.8640 (tp30) REVERT: B 15 LYS cc_start: 0.9246 (ptpt) cc_final: 0.8977 (ptpp) REVERT: B 155 ASN cc_start: 0.7812 (t0) cc_final: 0.7502 (t0) REVERT: B 226 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 280 LYS cc_start: 0.9075 (tttm) cc_final: 0.8625 (ttpp) REVERT: N 32 TYR cc_start: 0.8256 (m-80) cc_final: 0.7772 (m-80) REVERT: N 36 TRP cc_start: 0.8733 (m100) cc_final: 0.8500 (m100) REVERT: N 60 TYR cc_start: 0.8473 (m-80) cc_final: 0.8050 (m-80) REVERT: N 65 LYS cc_start: 0.8638 (tptm) cc_final: 0.8222 (tppp) REVERT: N 87 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7746 (mtmm) REVERT: N 90 ASP cc_start: 0.6609 (m-30) cc_final: 0.6191 (m-30) REVERT: N 114 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8769 (t) REVERT: R 227 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7949 (pt0) REVERT: R 229 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7182 (tm-30) outliers start: 25 outliers final: 17 residues processed: 194 average time/residue: 0.2546 time to fit residues: 63.9823 Evaluate side-chains 158 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 161 SER 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 N residue 84 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 303 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** R 282 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 = 0.3796 r_free = 0.3796 target = 0.106588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.082193 restraints weight = 16935.008| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.09 r_work: 0.3241 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8458 Z= 0.189 Angle : 0.738 30.805 11498 Z= 0.323 Chirality : 0.065 1.844 1320 Planarity : 0.004 0.056 1446 Dihedral : 11.533 169.997 1419 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.08 % Allowed : 13.68 % Favored : 83.24 % 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: -0.11 (0.26), residues: 1027 helix: 1.49 (0.26), residues: 394 sheet: -1.07 (0.32), residues: 223 loop : -0.97 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.017 0.001 PHE B 199 TYR 0.011 0.001 TYR N 115 ARG 0.005 0.001 ARG A 169 *********************** 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 179 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.892 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: 0.8033 (tt) cc_final: 0.7611 (pt) REVERT: A 230 ASP cc_start: 0.8388 (m-30) cc_final: 0.8151 (m-30) REVERT: B 9 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8787 (pp30) REVERT: B 10 GLU cc_start: 0.8936 (tp30) cc_final: 0.8576 (tp30) REVERT: B 15 LYS cc_start: 0.9242 (ptpt) cc_final: 0.9021 (ptpp) REVERT: B 23 LYS cc_start: 0.9239 (pttt) cc_final: 0.9011 (pttp) REVERT: B 35 ASN cc_start: 0.8693 (m110) cc_final: 0.8427 (m-40) REVERT: B 280 LYS cc_start: 0.9017 (tttm) cc_final: 0.8687 (tttm) REVERT: B 336 LEU cc_start: 0.8788 (tt) cc_final: 0.8486 (tt) REVERT: G 47 GLU cc_start: 0.8820 (mp0) cc_final: 0.8612 (mp0) REVERT: N 51 ILE cc_start: 0.7690 (pt) cc_final: 0.7323 (pt) REVERT: N 53 GLN cc_start: 0.8808 (mp10) cc_final: 0.8511 (mp10) REVERT: N 60 TYR cc_start: 0.8630 (m-80) cc_final: 0.8386 (m-80) REVERT: N 105 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7942 (mtp180) REVERT: R 96 LEU cc_start: 0.8355 (mt) cc_final: 0.8126 (mt) REVERT: R 227 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8002 (pt0) REVERT: R 229 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7266 (tm-30) outliers start: 27 outliers final: 21 residues processed: 170 average time/residue: 0.2544 time to fit residues: 56.4718 Evaluate side-chains 152 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 57 VAL 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 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP 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 70 ILE Chi-restraints excluded: chain N residue 84 ASN 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 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 67 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.104436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079548 restraints weight = 16732.970| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.10 r_work: 0.3174 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8458 Z= 0.220 Angle : 0.734 31.001 11498 Z= 0.322 Chirality : 0.065 1.827 1320 Planarity : 0.004 0.059 1446 Dihedral : 11.424 169.678 1419 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.42 % Allowed : 14.25 % Favored : 82.33 % 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: 0.17 (0.26), residues: 1027 helix: 1.62 (0.26), residues: 391 sheet: -0.95 (0.32), residues: 222 loop : -0.65 (0.31), residues: 414 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 0.015 0.001 PHE A 74 TYR 0.018 0.001 TYR R 308 ARG 0.004 0.000 ARG A 169 *********************** 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 171 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.835 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 60 MET cc_start: 0.5604 (tpt) cc_final: 0.5003 (mmm) REVERT: A 62 ILE cc_start: 0.8071 (tt) cc_final: 0.7553 (pt) REVERT: A 230 ASP cc_start: 0.8420 (m-30) cc_final: 0.8184 (m-30) REVERT: B 9 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8791 (pp30) REVERT: B 10 GLU cc_start: 0.8958 (tp30) cc_final: 0.8602 (tp30) REVERT: B 35 ASN cc_start: 0.8736 (m110) cc_final: 0.8499 (m-40) REVERT: B 129 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7643 (mmm160) REVERT: B 280 LYS cc_start: 0.9040 (tttm) cc_final: 0.8337 (ttmm) REVERT: G 22 GLU cc_start: 0.9045 (tp30) cc_final: 0.8545 (mm-30) REVERT: N 53 GLN cc_start: 0.8942 (mp10) cc_final: 0.8316 (mp10) REVERT: N 60 TYR cc_start: 0.8656 (m-80) cc_final: 0.8268 (m-80) REVERT: R 170 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7272 (mptt) REVERT: R 227 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8008 (pt0) REVERT: R 229 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7228 (tm-30) outliers start: 30 outliers final: 21 residues processed: 164 average time/residue: 0.2576 time to fit residues: 54.5586 Evaluate side-chains 150 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS 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 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 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 8 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.100416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075838 restraints weight = 16574.952| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.92 r_work: 0.3112 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8458 Z= 0.284 Angle : 0.766 31.164 11498 Z= 0.343 Chirality : 0.065 1.817 1320 Planarity : 0.004 0.061 1446 Dihedral : 11.481 169.659 1419 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.42 % Allowed : 14.60 % Favored : 81.98 % 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: 0.26 (0.26), residues: 1027 helix: 1.57 (0.26), residues: 391 sheet: -0.82 (0.32), residues: 223 loop : -0.51 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 211 HIS 0.003 0.001 HIS A 41 PHE 0.016 0.001 PHE A 74 TYR 0.009 0.001 TYR B 105 ARG 0.006 0.001 ARG N 72 *********************** 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 171 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.893 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 60 MET cc_start: 0.5664 (tpt) cc_final: 0.5109 (mmm) REVERT: A 62 ILE cc_start: 0.8148 (tt) cc_final: 0.7617 (pt) REVERT: A 230 ASP cc_start: 0.8418 (m-30) cc_final: 0.8208 (m-30) REVERT: B 9 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8830 (pp30) REVERT: B 10 GLU cc_start: 0.9021 (tp30) cc_final: 0.8636 (tp30) REVERT: B 35 ASN cc_start: 0.8784 (m110) cc_final: 0.8518 (m110) REVERT: B 129 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7813 (mmm160) REVERT: B 280 LYS cc_start: 0.9129 (tttm) cc_final: 0.8711 (ttpp) REVERT: G 22 GLU cc_start: 0.9024 (tp30) cc_final: 0.8738 (tp30) REVERT: N 53 GLN cc_start: 0.8864 (mp10) cc_final: 0.8407 (mp10) REVERT: N 60 TYR cc_start: 0.8614 (m-80) cc_final: 0.7465 (m-80) REVERT: R 170 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7331 (mptt) outliers start: 30 outliers final: 25 residues processed: 162 average time/residue: 0.2661 time to fit residues: 56.7717 Evaluate side-chains 151 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS 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 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 179 MET Chi-restraints excluded: chain R residue 190 CYS 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 56 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 62 optimal weight: 40.0000 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN B 88 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.100208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075504 restraints weight = 16819.042| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.83 r_work: 0.3087 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8458 Z= 0.280 Angle : 0.776 30.977 11498 Z= 0.346 Chirality : 0.065 1.808 1320 Planarity : 0.004 0.061 1446 Dihedral : 11.452 171.309 1419 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.53 % Allowed : 14.71 % Favored : 81.76 % 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: 0.34 (0.26), residues: 1027 helix: 1.56 (0.26), residues: 391 sheet: -0.71 (0.33), residues: 223 loop : -0.43 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 211 HIS 0.003 0.001 HIS A 209 PHE 0.015 0.001 PHE A 74 TYR 0.024 0.002 TYR R 299 ARG 0.004 0.000 ARG N 19 *********************** 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 167 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.922 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: 0.8165 (tt) cc_final: 0.7797 (pt) REVERT: B 9 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8853 (pp30) REVERT: B 10 GLU cc_start: 0.9016 (tp30) cc_final: 0.8620 (tp30) REVERT: B 129 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7835 (mmm160) REVERT: B 280 LYS cc_start: 0.9133 (tttm) cc_final: 0.8879 (tttm) REVERT: G 22 GLU cc_start: 0.8999 (tp30) cc_final: 0.8751 (tp30) REVERT: N 51 ILE cc_start: 0.7853 (pt) cc_final: 0.7600 (pt) REVERT: N 53 GLN cc_start: 0.8832 (mp10) cc_final: 0.8253 (mp10) REVERT: N 60 TYR cc_start: 0.8639 (m-80) cc_final: 0.7574 (m-80) REVERT: N 87 LYS cc_start: 0.8291 (tppt) cc_final: 0.8051 (ttmm) REVERT: R 39 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: R 170 LYS cc_start: 0.8390 (mmtt) cc_final: 0.7456 (mptt) outliers start: 31 outliers final: 26 residues processed: 158 average time/residue: 0.2583 time to fit residues: 52.6632 Evaluate side-chains 155 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 ASN 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 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS 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 39 GLN 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 179 MET Chi-restraints excluded: chain R residue 190 CYS 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 2 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 69 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.100629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.076017 restraints weight = 16891.409| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.87 r_work: 0.3104 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8458 Z= 0.239 Angle : 0.765 30.809 11498 Z= 0.340 Chirality : 0.065 1.809 1320 Planarity : 0.004 0.060 1446 Dihedral : 11.419 171.907 1419 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.53 % Allowed : 15.96 % Favored : 80.50 % 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: 0.53 (0.27), residues: 1027 helix: 1.69 (0.26), residues: 390 sheet: -0.59 (0.33), residues: 222 loop : -0.29 (0.33), residues: 415 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 0.020 0.001 TYR N 115 ARG 0.007 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 169 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.977 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: 0.8254 (tt) cc_final: 0.7826 (pt) REVERT: B 9 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8875 (pp30) REVERT: B 10 GLU cc_start: 0.9018 (tp30) cc_final: 0.8623 (tp30) REVERT: G 22 GLU cc_start: 0.8988 (tp30) cc_final: 0.8740 (tp30) REVERT: N 38 ARG cc_start: 0.8557 (ptt-90) cc_final: 0.8279 (ptt90) REVERT: N 46 GLU cc_start: 0.7637 (tt0) cc_final: 0.7286 (tt0) REVERT: N 53 GLN cc_start: 0.8797 (mp10) cc_final: 0.8170 (mp10) REVERT: N 60 TYR cc_start: 0.8643 (m-80) cc_final: 0.7531 (m-80) REVERT: R 39 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7264 (mp10) REVERT: R 170 LYS cc_start: 0.8398 (mmtt) cc_final: 0.7445 (mptt) REVERT: R 173 PHE cc_start: 0.8292 (t80) cc_final: 0.8006 (t80) REVERT: R 265 LYS cc_start: 0.6978 (tppt) cc_final: 0.6615 (ttpt) outliers start: 31 outliers final: 23 residues processed: 161 average time/residue: 0.2578 time to fit residues: 54.0488 Evaluate side-chains 155 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 ASN 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 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 39 GLN 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 190 CYS 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 84 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 0.0770 chunk 5 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.102967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.078427 restraints weight = 16858.013| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.89 r_work: 0.3203 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8458 Z= 0.172 Angle : 0.744 30.562 11498 Z= 0.329 Chirality : 0.064 1.813 1320 Planarity : 0.004 0.060 1446 Dihedral : 11.328 172.772 1419 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.96 % Allowed : 16.76 % Favored : 80.27 % 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 (0.27), residues: 1027 helix: 1.79 (0.26), residues: 390 sheet: -0.34 (0.35), residues: 200 loop : -0.22 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.000 HIS A 209 PHE 0.015 0.001 PHE B 199 TYR 0.019 0.001 TYR N 115 ARG 0.007 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 to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8231 (tt) cc_final: 0.7812 (pt) REVERT: A 230 ASP cc_start: 0.8489 (m-30) cc_final: 0.8250 (m-30) REVERT: B 9 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8829 (pp30) REVERT: B 10 GLU cc_start: 0.8957 (tp30) cc_final: 0.8540 (tp30) REVERT: B 35 ASN cc_start: 0.8794 (m110) cc_final: 0.8423 (m110) REVERT: B 280 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8543 (ttmm) REVERT: B 289 TYR cc_start: 0.8981 (m-80) cc_final: 0.8449 (m-80) REVERT: B 297 TRP cc_start: 0.8441 (m100) cc_final: 0.7881 (m100) REVERT: B 336 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8648 (tt) REVERT: G 22 GLU cc_start: 0.8927 (tp30) cc_final: 0.8709 (tp30) REVERT: G 29 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8616 (mmmt) REVERT: G 32 LYS cc_start: 0.8908 (tppt) cc_final: 0.8657 (tppt) REVERT: G 47 GLU cc_start: 0.8872 (mp0) cc_final: 0.8629 (mp0) REVERT: N 5 GLN cc_start: 0.7775 (mp10) cc_final: 0.7511 (mp10) REVERT: N 19 ARG cc_start: 0.8447 (ttt90) cc_final: 0.8161 (ttt90) REVERT: N 38 ARG cc_start: 0.8584 (ptt-90) cc_final: 0.8222 (ptt90) REVERT: N 46 GLU cc_start: 0.7644 (tt0) cc_final: 0.7299 (tt0) REVERT: N 51 ILE cc_start: 0.7658 (pt) cc_final: 0.7456 (pt) REVERT: N 53 GLN cc_start: 0.8741 (mp10) cc_final: 0.8241 (mp10) REVERT: N 60 TYR cc_start: 0.8636 (m-80) cc_final: 0.8209 (m-80) REVERT: N 78 THR cc_start: 0.9022 (m) cc_final: 0.8351 (p) REVERT: N 80 TYR cc_start: 0.8278 (m-80) cc_final: 0.7539 (m-80) REVERT: N 87 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7894 (mmtp) REVERT: N 122 THR cc_start: 0.8344 (m) cc_final: 0.7913 (p) REVERT: R 170 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7372 (mptt) REVERT: R 173 PHE cc_start: 0.8161 (t80) cc_final: 0.7869 (t80) outliers start: 26 outliers final: 18 residues processed: 168 average time/residue: 0.2333 time to fit residues: 51.8227 Evaluate side-chains 156 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 101 VAL 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 69 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 61 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** R 286 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 = 0.3737 r_free = 0.3737 target = 0.102007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.077549 restraints weight = 16865.643| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.88 r_work: 0.3176 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8458 Z= 0.204 Angle : 0.758 30.708 11498 Z= 0.336 Chirality : 0.065 1.816 1320 Planarity : 0.004 0.060 1446 Dihedral : 11.309 171.635 1419 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.85 % Allowed : 17.56 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 1027 helix: 1.77 (0.26), residues: 391 sheet: -0.36 (0.33), residues: 223 loop : -0.26 (0.33), residues: 413 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 0.014 0.001 PHE A 74 TYR 0.020 0.001 TYR N 115 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 165 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.908 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: 0.8285 (tt) cc_final: 0.7956 (pt) REVERT: B 9 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8874 (pp30) REVERT: B 10 GLU cc_start: 0.8994 (tp30) cc_final: 0.8618 (tp30) REVERT: B 35 ASN cc_start: 0.8890 (m110) cc_final: 0.8528 (m-40) REVERT: B 280 LYS cc_start: 0.9061 (ttpp) cc_final: 0.8523 (ttmm) REVERT: G 22 GLU cc_start: 0.8992 (tp30) cc_final: 0.8752 (tp30) REVERT: G 32 LYS cc_start: 0.8950 (tppt) cc_final: 0.8678 (tppt) REVERT: G 47 GLU cc_start: 0.8911 (mp0) cc_final: 0.8634 (mp0) REVERT: N 19 ARG cc_start: 0.8484 (ttt90) cc_final: 0.8198 (ttt90) REVERT: N 38 ARG cc_start: 0.8565 (ptt-90) cc_final: 0.8190 (ptt90) REVERT: N 46 GLU cc_start: 0.7669 (tt0) cc_final: 0.7274 (tt0) REVERT: N 51 ILE cc_start: 0.7665 (pt) cc_final: 0.7403 (pt) REVERT: N 53 GLN cc_start: 0.8676 (mp10) cc_final: 0.8138 (mp10) REVERT: N 60 TYR cc_start: 0.8679 (m-80) cc_final: 0.8208 (m-80) REVERT: N 78 THR cc_start: 0.8970 (m) cc_final: 0.8312 (p) REVERT: N 80 TYR cc_start: 0.8251 (m-80) cc_final: 0.7503 (m-80) REVERT: N 87 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7830 (mmtp) REVERT: N 122 THR cc_start: 0.8292 (m) cc_final: 0.7840 (p) REVERT: R 170 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7409 (mptt) REVERT: R 173 PHE cc_start: 0.8098 (t80) cc_final: 0.7792 (t80) outliers start: 25 outliers final: 22 residues processed: 157 average time/residue: 0.2337 time to fit residues: 48.4418 Evaluate side-chains 153 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 ASN 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 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 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 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 24 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 86 optimal weight: 0.0980 chunk 67 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076293 restraints weight = 16936.659| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.92 r_work: 0.3128 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8458 Z= 0.197 Angle : 0.760 30.626 11498 Z= 0.339 Chirality : 0.064 1.810 1320 Planarity : 0.004 0.060 1446 Dihedral : 11.294 172.548 1419 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.39 % Allowed : 18.59 % Favored : 79.02 % 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: 0.67 (0.27), residues: 1027 helix: 1.74 (0.26), residues: 392 sheet: -0.39 (0.34), residues: 224 loop : -0.24 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 36 HIS 0.003 0.001 HIS A 209 PHE 0.014 0.001 PHE A 74 TYR 0.021 0.001 TYR N 115 ARG 0.011 0.000 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 159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.925 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: 0.8363 (tt) cc_final: 0.7931 (pt) REVERT: A 64 HIS cc_start: 0.7178 (t70) cc_final: 0.6959 (t-90) REVERT: B 9 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8897 (pp30) REVERT: B 10 GLU cc_start: 0.9013 (tp30) cc_final: 0.8642 (tp30) REVERT: B 35 ASN cc_start: 0.8706 (m110) cc_final: 0.8347 (m-40) REVERT: B 262 MET cc_start: 0.7955 (tpp) cc_final: 0.7642 (mmm) REVERT: B 280 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8547 (ttmm) REVERT: B 289 TYR cc_start: 0.8949 (m-80) cc_final: 0.8531 (m-80) REVERT: B 336 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8678 (tt) REVERT: G 22 GLU cc_start: 0.9026 (tp30) cc_final: 0.8776 (tp30) REVERT: G 29 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8754 (tppt) REVERT: G 32 LYS cc_start: 0.8994 (tppt) cc_final: 0.8745 (tppt) REVERT: G 47 GLU cc_start: 0.8888 (mp0) cc_final: 0.8621 (mp0) REVERT: N 5 GLN cc_start: 0.7891 (mp10) cc_final: 0.7544 (mp10) REVERT: N 19 ARG cc_start: 0.8511 (ttt90) cc_final: 0.8224 (ttt90) REVERT: N 38 ARG cc_start: 0.8552 (ptt-90) cc_final: 0.8192 (ptt90) REVERT: N 46 GLU cc_start: 0.7742 (tt0) cc_final: 0.7376 (tt0) REVERT: N 53 GLN cc_start: 0.8653 (mp10) cc_final: 0.8102 (mp10) REVERT: N 60 TYR cc_start: 0.8691 (m-80) cc_final: 0.8192 (m-80) REVERT: N 78 THR cc_start: 0.8878 (m) cc_final: 0.8265 (p) REVERT: N 80 TYR cc_start: 0.8191 (m-80) cc_final: 0.7371 (m-80) REVERT: N 87 LYS cc_start: 0.8321 (mmmt) cc_final: 0.8015 (mmtp) REVERT: N 122 THR cc_start: 0.8310 (m) cc_final: 0.7984 (p) REVERT: R 170 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7361 (mptt) REVERT: R 173 PHE cc_start: 0.8087 (t80) cc_final: 0.7787 (t80) outliers start: 21 outliers final: 20 residues processed: 153 average time/residue: 0.2409 time to fit residues: 48.9513 Evaluate side-chains 155 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 ASN 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 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 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 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 16 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 36 ASN ** R 286 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 = 0.3702 r_free = 0.3702 target = 0.100925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076361 restraints weight = 17148.996| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.96 r_work: 0.3135 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8458 Z= 0.189 Angle : 0.754 30.592 11498 Z= 0.336 Chirality : 0.064 1.811 1320 Planarity : 0.004 0.060 1446 Dihedral : 11.254 172.620 1419 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.85 % Allowed : 18.13 % Favored : 79.02 % 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: 0.69 (0.27), residues: 1027 helix: 1.74 (0.26), residues: 392 sheet: -0.35 (0.34), residues: 224 loop : -0.23 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 36 HIS 0.003 0.000 HIS A 209 PHE 0.013 0.001 PHE A 74 TYR 0.023 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: 4392.22 seconds wall clock time: 78 minutes 44.30 seconds (4724.30 seconds total)