Starting phenix.real_space_refine on Sat Aug 3 13:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/08_2024/8w8a_37350.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/08_2024/8w8a_37350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/08_2024/8w8a_37350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/08_2024/8w8a_37350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/08_2024/8w8a_37350.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/08_2024/8w8a_37350.cif" } resolution = 2.8 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= 0.026 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 63 5.16 5 C 5250 2.51 5 N 1422 2.21 5 O 1525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "R ARG 83": "NH1" <-> "NH2" Residue "R TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 162": "OE1" <-> "OE2" Residue "R PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8260 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1934 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2597 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Unusual residues: {'T5U': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.10, per 1000 atoms: 0.62 Number of scatterers: 8260 At special positions: 0 Unit cell: (79.04, 99.84, 133.12, 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 63 16.00 O 1525 8.00 N 1422 7.00 C 5250 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=2.27 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.35 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.35 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: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 44.0% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 12 through 37 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.752A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.129A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 205 removed outlier: 3.690A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) 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 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.575A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.724A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 51 Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 86 removed outlier: 3.685A pdb=" N VAL R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 127 Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 187 through 199 removed outlier: 3.562A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 232 Processing helix chain 'R' and resid 247 through 274 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 276 through 280 Processing helix chain 'R' and resid 282 through 306 removed outlier: 3.543A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR R 298 " --> pdb=" O TYR R 294 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 318 removed outlier: 3.616A pdb=" N ARG R 312 " --> pdb=" O TYR R 308 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75 removed outlier: 4.880A pdb=" N VAL A 86 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLY A 47 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.616A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.753A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.976A 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 105 removed outlier: 6.852A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.512A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.719A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.457A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.870A 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: 6.427A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.588A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 18 through 20 435 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: 2.47 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1394 1.32 - 1.44: 2329 1.44 - 1.56: 4624 1.56 - 1.69: 2 1.69 - 1.81: 92 Bond restraints: 8441 Sorted by residual: bond pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 1.524 1.447 0.077 1.25e-02 6.40e+03 3.78e+01 bond pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.04e-02 9.25e+03 2.40e+01 bond pdb=" C13 T5U R 401 " pdb=" N03 T5U R 401 " ideal model delta sigma weight residual 1.275 1.354 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" CA SER R 183 " pdb=" C SER R 183 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.08e-02 8.57e+03 1.54e+01 bond pdb=" CA LYS B 57 " pdb=" C LYS B 57 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.26e-02 6.30e+03 1.46e+01 ... (remaining 8436 not shown) Histogram of bond angle deviations from ideal: 99.91 - 107.25: 273 107.25 - 114.59: 4896 114.59 - 121.93: 4598 121.93 - 129.27: 1596 129.27 - 136.61: 69 Bond angle restraints: 11432 Sorted by residual: angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 109.71 119.49 -9.78 1.41e+00 5.03e-01 4.81e+01 angle pdb=" N ASN A 66 " pdb=" CA ASN A 66 " pdb=" C ASN A 66 " ideal model delta sigma weight residual 111.30 101.74 9.56 1.43e+00 4.89e-01 4.47e+01 angle pdb=" N CYS N 96 " pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 110.17 100.08 10.09 1.61e+00 3.86e-01 3.93e+01 angle pdb=" N GLY A 68 " pdb=" CA GLY A 68 " pdb=" C GLY A 68 " ideal model delta sigma weight residual 112.49 119.46 -6.97 1.21e+00 6.83e-01 3.32e+01 angle pdb=" N HIS A 64 " pdb=" CA HIS A 64 " pdb=" C HIS A 64 " ideal model delta sigma weight residual 110.06 102.44 7.62 1.43e+00 4.89e-01 2.84e+01 ... (remaining 11427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4581 17.53 - 35.07: 362 35.07 - 52.60: 66 52.60 - 70.14: 14 70.14 - 87.67: 3 Dihedral angle restraints: 5026 sinusoidal: 1979 harmonic: 3047 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual 93.00 179.74 -86.74 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 160.94 -67.94 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" C CYS N 96 " pdb=" N CYS N 96 " pdb=" CA CYS N 96 " pdb=" CB CYS N 96 " ideal model delta harmonic sigma weight residual -122.60 -109.09 -13.51 0 2.50e+00 1.60e-01 2.92e+01 ... (remaining 5023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1025 0.059 - 0.117: 200 0.117 - 0.176: 36 0.176 - 0.234: 8 0.234 - 0.293: 6 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA LYS A 126 " pdb=" N LYS A 126 " pdb=" C LYS A 126 " pdb=" CB LYS A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA MET A 60 " pdb=" N MET A 60 " pdb=" C MET A 60 " pdb=" CB MET A 60 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA GLU R 162 " pdb=" N GLU R 162 " pdb=" C GLU R 162 " pdb=" CB GLU R 162 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1272 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR N 94 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C TYR N 94 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR N 94 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR N 95 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 57 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C LYS B 57 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS B 57 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE B 58 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 125 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C PHE A 125 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE A 125 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 126 " -0.012 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2228 2.80 - 3.33: 7744 3.33 - 3.85: 14024 3.85 - 4.38: 16667 4.38 - 4.90: 29104 Nonbonded interactions: 69767 Sorted by model distance: nonbonded pdb=" NH2 ARG A 90 " pdb=" OD1 ASP B 186 " model vdw 2.280 3.120 nonbonded pdb=" OH TYR B 59 " pdb=" OE1 GLN B 75 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.292 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.303 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.320 3.040 ... (remaining 69762 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: 2.220 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 8441 Z= 0.340 Angle : 0.712 11.611 11432 Z= 0.428 Chirality : 0.053 0.293 1275 Planarity : 0.004 0.039 1456 Dihedral : 12.995 87.674 3049 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.89 % Allowed : 1.12 % Favored : 97.99 % Cbeta Deviations : 0.10 % 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: 0.81 (0.27), residues: 1033 helix: 2.09 (0.26), residues: 409 sheet: -0.20 (0.35), residues: 213 loop : -0.61 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 89 HIS 0.005 0.001 HIS A 209 PHE 0.027 0.002 PHE R 185 TYR 0.016 0.001 TYR N 60 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 0.992 Fit side-chains REVERT: N 3 GLN cc_start: 0.8194 (pt0) cc_final: 0.7623 (pt0) REVERT: R 60 TRP cc_start: 0.8292 (m100) cc_final: 0.8079 (m100) outliers start: 8 outliers final: 2 residues processed: 174 average time/residue: 1.1851 time to fit residues: 219.3872 Evaluate side-chains 132 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 225 SER 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: 5.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 130 ASN A 146 GLN G 24 ASN R 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8441 Z= 0.209 Angle : 0.526 6.381 11432 Z= 0.281 Chirality : 0.042 0.134 1275 Planarity : 0.004 0.038 1456 Dihedral : 4.898 43.499 1160 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.24 % Allowed : 11.74 % Favored : 86.02 % 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: 0.99 (0.27), residues: 1033 helix: 2.35 (0.26), residues: 409 sheet: -0.18 (0.37), residues: 193 loop : -0.58 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.014 0.001 PHE B 292 TYR 0.012 0.001 TYR R 279 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 0.974 Fit side-chains REVERT: B 19 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7666 (ttp-110) REVERT: N 3 GLN cc_start: 0.8163 (pt0) cc_final: 0.7552 (pt0) REVERT: R 302 MET cc_start: 0.7901 (mtt) cc_final: 0.7689 (mtt) outliers start: 20 outliers final: 8 residues processed: 147 average time/residue: 1.2333 time to fit residues: 192.7860 Evaluate side-chains 130 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 0.0020 chunk 25 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 73 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8441 Z= 0.148 Angle : 0.478 6.906 11432 Z= 0.253 Chirality : 0.041 0.146 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.264 24.721 1158 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.13 % Allowed : 13.87 % Favored : 84.00 % 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: 1.14 (0.27), residues: 1033 helix: 2.46 (0.26), residues: 410 sheet: -0.18 (0.37), residues: 195 loop : -0.46 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.010 0.001 PHE R 267 TYR 0.012 0.001 TYR R 308 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.964 Fit side-chains REVERT: B 59 TYR cc_start: 0.8220 (m-80) cc_final: 0.7995 (m-80) REVERT: N 3 GLN cc_start: 0.8153 (pt0) cc_final: 0.7556 (pt0) REVERT: R 83 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6254 (ttm170) outliers start: 19 outliers final: 12 residues processed: 144 average time/residue: 1.1882 time to fit residues: 182.2920 Evaluate side-chains 133 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 97 optimal weight: 0.0370 chunk 48 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8441 Z= 0.136 Angle : 0.473 8.473 11432 Z= 0.248 Chirality : 0.041 0.136 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.105 24.446 1158 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.46 % Allowed : 15.66 % Favored : 81.88 % 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: 1.20 (0.27), residues: 1033 helix: 2.58 (0.26), residues: 408 sheet: -0.12 (0.36), residues: 188 loop : -0.51 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 55 PHE 0.010 0.001 PHE R 267 TYR 0.010 0.001 TYR R 308 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 0.884 Fit side-chains REVERT: B 19 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7709 (ttp-110) REVERT: G 21 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8109 (mpp) REVERT: N 3 GLN cc_start: 0.8142 (pt0) cc_final: 0.7557 (pt0) REVERT: R 83 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6184 (ttm170) outliers start: 22 outliers final: 10 residues processed: 142 average time/residue: 1.1219 time to fit residues: 170.0079 Evaluate side-chains 131 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8441 Z= 0.209 Angle : 0.504 8.999 11432 Z= 0.263 Chirality : 0.042 0.141 1275 Planarity : 0.003 0.038 1456 Dihedral : 4.261 24.572 1158 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.13 % Allowed : 16.78 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.27), residues: 1033 helix: 2.54 (0.26), residues: 408 sheet: -0.15 (0.36), residues: 198 loop : -0.54 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.011 0.001 PHE R 267 TYR 0.012 0.001 TYR R 308 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 0.829 Fit side-chains REVERT: B 19 ARG cc_start: 0.8046 (ttm110) cc_final: 0.7737 (ttp-110) REVERT: G 17 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: N 3 GLN cc_start: 0.8187 (pt0) cc_final: 0.7591 (pt0) REVERT: R 83 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6275 (ttm170) outliers start: 28 outliers final: 15 residues processed: 146 average time/residue: 1.1131 time to fit residues: 173.6566 Evaluate side-chains 134 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 0.0770 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8441 Z= 0.156 Angle : 0.491 10.039 11432 Z= 0.255 Chirality : 0.041 0.187 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.114 24.290 1158 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.02 % Allowed : 17.00 % Favored : 79.98 % 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: 1.20 (0.27), residues: 1033 helix: 2.59 (0.26), residues: 408 sheet: -0.08 (0.36), residues: 198 loop : -0.53 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.010 0.001 PHE R 267 TYR 0.015 0.001 TYR N 80 ARG 0.002 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 0.941 Fit side-chains REVERT: A 34 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: B 59 TYR cc_start: 0.8293 (m-80) cc_final: 0.8047 (m-10) REVERT: G 21 MET cc_start: 0.8437 (mpp) cc_final: 0.8127 (mpp) REVERT: N 3 GLN cc_start: 0.8178 (pt0) cc_final: 0.7549 (pt0) REVERT: N 85 SER cc_start: 0.8928 (m) cc_final: 0.8586 (p) REVERT: R 83 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6210 (ttm170) outliers start: 27 outliers final: 14 residues processed: 145 average time/residue: 1.2128 time to fit residues: 186.8523 Evaluate side-chains 135 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 277 LEU 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: 6.9990 chunk 71 optimal weight: 0.0970 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8441 Z= 0.190 Angle : 0.510 11.099 11432 Z= 0.263 Chirality : 0.042 0.168 1275 Planarity : 0.003 0.048 1456 Dihedral : 4.179 24.328 1158 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.68 % Allowed : 17.56 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1033 helix: 2.56 (0.26), residues: 408 sheet: -0.14 (0.35), residues: 206 loop : -0.44 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.011 0.001 PHE R 267 TYR 0.012 0.001 TYR R 308 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 0.965 Fit side-chains REVERT: A 34 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6790 (tt0) REVERT: B 19 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7762 (ttp-110) REVERT: G 21 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8060 (mpp) REVERT: N 3 GLN cc_start: 0.8179 (pt0) cc_final: 0.7559 (pt0) REVERT: N 85 SER cc_start: 0.8928 (m) cc_final: 0.8592 (p) REVERT: R 83 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6192 (ttm170) REVERT: R 88 CYS cc_start: 0.8175 (t) cc_final: 0.7632 (t) outliers start: 24 outliers final: 15 residues processed: 143 average time/residue: 1.1832 time to fit residues: 180.6047 Evaluate side-chains 140 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8441 Z= 0.176 Angle : 0.501 7.565 11432 Z= 0.261 Chirality : 0.042 0.161 1275 Planarity : 0.003 0.046 1456 Dihedral : 4.149 24.344 1158 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.35 % Allowed : 18.90 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1033 helix: 2.57 (0.26), residues: 408 sheet: -0.15 (0.35), residues: 210 loop : -0.44 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.010 0.001 PHE R 267 TYR 0.013 0.001 TYR N 80 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.984 Fit side-chains REVERT: A 34 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6789 (tt0) REVERT: G 21 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8062 (mpp) REVERT: N 3 GLN cc_start: 0.8179 (pt0) cc_final: 0.7545 (pt0) REVERT: R 83 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6118 (ttm170) outliers start: 21 outliers final: 16 residues processed: 137 average time/residue: 1.1629 time to fit residues: 170.0290 Evaluate side-chains 138 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8441 Z= 0.218 Angle : 0.530 13.091 11432 Z= 0.274 Chirality : 0.043 0.153 1275 Planarity : 0.003 0.038 1456 Dihedral : 4.238 24.585 1158 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.46 % Allowed : 19.24 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1033 helix: 2.50 (0.26), residues: 408 sheet: -0.19 (0.36), residues: 205 loop : -0.43 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.004 0.001 HIS R 63 PHE 0.011 0.001 PHE B 292 TYR 0.012 0.001 TYR R 308 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.970 Fit side-chains REVERT: A 34 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6812 (tt0) REVERT: B 19 ARG cc_start: 0.8123 (ttp-110) cc_final: 0.7829 (ttp-110) REVERT: G 21 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8072 (mpp) REVERT: N 3 GLN cc_start: 0.8174 (pt0) cc_final: 0.7538 (pt0) REVERT: N 120 GLN cc_start: 0.8297 (mm110) cc_final: 0.7951 (mm-40) REVERT: R 83 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6163 (ttm170) outliers start: 22 outliers final: 17 residues processed: 133 average time/residue: 1.2664 time to fit residues: 179.4060 Evaluate side-chains 138 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8441 Z= 0.198 Angle : 0.518 7.982 11432 Z= 0.270 Chirality : 0.042 0.150 1275 Planarity : 0.003 0.038 1456 Dihedral : 4.227 24.641 1158 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.13 % Allowed : 19.80 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.27), residues: 1033 helix: 2.52 (0.26), residues: 408 sheet: -0.17 (0.36), residues: 205 loop : -0.43 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.011 0.001 PHE B 292 TYR 0.013 0.001 TYR N 80 ARG 0.005 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 0.941 Fit side-chains REVERT: A 34 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: B 19 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7754 (ttp-110) REVERT: N 3 GLN cc_start: 0.8175 (pt0) cc_final: 0.7542 (pt0) REVERT: N 120 GLN cc_start: 0.8262 (mm110) cc_final: 0.7915 (mm-40) REVERT: R 83 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6087 (ttm170) outliers start: 19 outliers final: 13 residues processed: 132 average time/residue: 1.1881 time to fit residues: 167.1808 Evaluate side-chains 134 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.149697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.112340 restraints weight = 9668.618| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.27 r_work: 0.3186 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8441 Z= 0.180 Angle : 0.517 9.229 11432 Z= 0.267 Chirality : 0.042 0.149 1275 Planarity : 0.003 0.038 1456 Dihedral : 4.173 24.507 1158 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.24 % Allowed : 19.80 % Favored : 77.96 % 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: 1.19 (0.27), residues: 1033 helix: 2.50 (0.26), residues: 410 sheet: -0.15 (0.36), residues: 205 loop : -0.42 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.003 0.001 HIS A 41 PHE 0.011 0.001 PHE B 292 TYR 0.012 0.001 TYR R 308 ARG 0.005 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3529.13 seconds wall clock time: 62 minutes 24.87 seconds (3744.87 seconds total)