Starting phenix.real_space_refine on Fri Jul 19 14:29:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/07_2024/8w8a_37350.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/07_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_37350/07_2024/8w8a_37350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/07_2024/8w8a_37350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/07_2024/8w8a_37350.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/07_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-5388/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: 5.14, 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: 3.10 Conformation dependent library (CDL) restraints added in 1.5 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: 0.81 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: 2.50 Time building geometry restraints manager: 3.36 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 2.520 nonbonded pdb=" OH TYR B 59 " pdb=" OE1 GLN B 75 " model vdw 2.290 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.292 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.303 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.320 2.440 ... (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 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 25.460 Find NCS groups from input model: 0.090 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:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.840 ------------------------------------------------------------------------------- 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 : 0.919 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: 1.1228 time to fit residues: 208.0590 Evaluate side-chains 132 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- 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: 0.8107 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 : 0.004 0.031 8441 Z= 0.257 Angle : 0.536 6.338 11432 Z= 0.284 Chirality : 0.043 0.135 1275 Planarity : 0.004 0.038 1456 Dihedral : 4.883 33.529 1160 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.02 % Allowed : 11.19 % Favored : 85.79 % 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: 1.00 (0.27), residues: 1033 helix: 2.32 (0.26), residues: 409 sheet: -0.16 (0.36), residues: 198 loop : -0.55 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 PHE 0.015 0.002 PHE B 292 TYR 0.013 0.002 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 161 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 0.897 Fit side-chains REVERT: B 19 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7665 (ttp-110) REVERT: N 3 GLN cc_start: 0.8151 (pt0) cc_final: 0.7546 (pt0) REVERT: R 302 MET cc_start: 0.7925 (mtt) cc_final: 0.7682 (mtt) outliers start: 27 outliers final: 15 residues processed: 147 average time/residue: 1.1475 time to fit residues: 180.0509 Evaluate side-chains 138 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER 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 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 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: 1.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1370 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= 0.223 Angle : 0.504 7.031 11432 Z= 0.266 Chirality : 0.042 0.142 1275 Planarity : 0.003 0.038 1456 Dihedral : 4.518 28.133 1159 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.46 % Allowed : 13.65 % Favored : 83.89 % 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: 1.02 (0.27), residues: 1033 helix: 2.35 (0.26), residues: 410 sheet: -0.22 (0.36), residues: 201 loop : -0.52 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.012 0.001 PHE B 292 TYR 0.013 0.001 TYR R 308 ARG 0.004 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: 22 poor density : 129 time to evaluate : 0.887 Fit side-chains REVERT: B 137 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7027 (ttp-170) REVERT: N 3 GLN cc_start: 0.8177 (pt0) cc_final: 0.7571 (pt0) REVERT: R 83 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6278 (ttm170) outliers start: 22 outliers final: 14 residues processed: 138 average time/residue: 1.2167 time to fit residues: 178.5408 Evaluate side-chains 135 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain N residue 7 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: 3.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.8134 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8441 Z= 0.288 Angle : 0.535 8.380 11432 Z= 0.280 Chirality : 0.043 0.142 1275 Planarity : 0.003 0.037 1456 Dihedral : 4.588 27.933 1158 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.58 % Allowed : 14.77 % Favored : 81.66 % 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: 0.98 (0.27), residues: 1033 helix: 2.37 (0.26), residues: 404 sheet: -0.12 (0.37), residues: 188 loop : -0.61 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.013 0.002 PHE R 267 TYR 0.013 0.002 TYR R 308 ARG 0.005 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 158 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.105 Fit side-chains REVERT: B 19 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7709 (ttp-110) REVERT: B 137 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7068 (ttp-110) REVERT: N 3 GLN cc_start: 0.8214 (pt0) cc_final: 0.7629 (pt0) REVERT: R 83 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6296 (ttm170) outliers start: 32 outliers final: 17 residues processed: 141 average time/residue: 1.1943 time to fit residues: 179.1947 Evaluate side-chains 133 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 83 MET 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: 2.9990 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.0070 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8441 Z= 0.162 Angle : 0.478 7.338 11432 Z= 0.250 Chirality : 0.042 0.188 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.280 26.658 1158 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.80 % Allowed : 17.45 % 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: 1.14 (0.27), residues: 1033 helix: 2.53 (0.26), residues: 404 sheet: -0.08 (0.36), residues: 193 loop : -0.54 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.012 0.001 PHE R 91 TYR 0.013 0.001 TYR R 308 ARG 0.004 0.000 ARG N 118 *********************** 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 151 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.887 Fit side-chains REVERT: A 132 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7854 (ttm110) REVERT: B 19 ARG cc_start: 0.8002 (ttm110) cc_final: 0.7678 (ttp-110) REVERT: B 137 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6260 (ttp-170) REVERT: N 3 GLN cc_start: 0.8206 (pt0) cc_final: 0.7625 (pt0) REVERT: R 83 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6183 (ttm170) outliers start: 25 outliers final: 12 residues processed: 136 average time/residue: 1.1700 time to fit residues: 169.3845 Evaluate side-chains 133 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain N residue 7 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.0370 chunk 94 optimal weight: 0.0030 overall best weight: 1.0072 ------------------------------------------------------------------------------- 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: 0.8108 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8441 Z= 0.210 Angle : 0.502 7.075 11432 Z= 0.261 Chirality : 0.042 0.143 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.299 26.524 1158 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.02 % Allowed : 18.01 % Favored : 78.97 % 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: 1.13 (0.27), residues: 1033 helix: 2.53 (0.26), residues: 404 sheet: -0.18 (0.36), residues: 190 loop : -0.51 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.011 0.001 PHE R 267 TYR 0.012 0.001 TYR R 308 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 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 144 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 0.852 Fit side-chains REVERT: A 132 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7881 (ttm110) REVERT: B 19 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7703 (ttp-110) REVERT: B 137 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.7047 (ttp-170) REVERT: N 3 GLN cc_start: 0.8145 (pt0) cc_final: 0.7573 (pt0) REVERT: R 83 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6169 (ttm170) outliers start: 27 outliers final: 12 residues processed: 132 average time/residue: 1.2098 time to fit residues: 169.6900 Evaluate side-chains 129 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain N residue 7 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 225 SER 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: 5.9990 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8441 Z= 0.171 Angle : 0.481 7.338 11432 Z= 0.249 Chirality : 0.041 0.136 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.185 26.538 1158 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.02 % Allowed : 18.34 % Favored : 78.64 % 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: 2.61 (0.26), residues: 404 sheet: -0.19 (0.35), residues: 203 loop : -0.42 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 89 HIS 0.004 0.001 HIS R 63 PHE 0.018 0.001 PHE R 91 TYR 0.012 0.001 TYR R 308 ARG 0.002 0.000 ARG N 118 *********************** 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: 27 poor density : 125 time to evaluate : 0.983 Fit side-chains REVERT: A 132 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7858 (ttm110) REVERT: B 137 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6252 (ttp-170) REVERT: G 21 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8113 (mpp) REVERT: N 3 GLN cc_start: 0.8173 (pt0) cc_final: 0.7613 (pt0) REVERT: R 83 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6058 (ttm170) outliers start: 27 outliers final: 17 residues processed: 138 average time/residue: 1.1556 time to fit residues: 170.3358 Evaluate side-chains 137 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8094 moved from start: 0.1723 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= 0.179 Angle : 0.492 8.237 11432 Z= 0.253 Chirality : 0.041 0.136 1275 Planarity : 0.003 0.046 1456 Dihedral : 4.179 26.267 1158 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.02 % Allowed : 18.23 % 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: 1.23 (0.27), residues: 1033 helix: 2.61 (0.26), residues: 404 sheet: -0.20 (0.35), residues: 203 loop : -0.40 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 89 HIS 0.004 0.001 HIS A 209 PHE 0.010 0.001 PHE R 267 TYR 0.012 0.001 TYR R 308 ARG 0.012 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 152 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 0.970 Fit side-chains REVERT: A 132 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7873 (ttm110) REVERT: B 19 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7719 (ttp-110) REVERT: G 21 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8057 (mpp) REVERT: N 3 GLN cc_start: 0.8148 (pt0) cc_final: 0.7577 (pt0) REVERT: R 83 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6024 (ttm170) outliers start: 27 outliers final: 21 residues processed: 139 average time/residue: 1.1950 time to fit residues: 177.1088 Evaluate side-chains 142 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 225 SER 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: 3.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1769 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= 0.189 Angle : 0.501 8.401 11432 Z= 0.257 Chirality : 0.042 0.136 1275 Planarity : 0.003 0.051 1456 Dihedral : 4.196 26.126 1158 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.91 % Allowed : 18.57 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1033 helix: 2.60 (0.26), residues: 404 sheet: -0.25 (0.35), residues: 208 loop : -0.37 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 89 HIS 0.004 0.001 HIS A 209 PHE 0.017 0.001 PHE R 91 TYR 0.022 0.001 TYR N 60 ARG 0.011 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 149 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 0.833 Fit side-chains REVERT: A 132 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7870 (ttm110) REVERT: G 21 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8092 (mpp) REVERT: N 3 GLN cc_start: 0.8173 (pt0) cc_final: 0.7608 (pt0) REVERT: R 83 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6009 (ttm170) outliers start: 26 outliers final: 18 residues processed: 137 average time/residue: 1.1285 time to fit residues: 165.1766 Evaluate side-chains 140 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 49 SER 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 225 SER Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 290 ILE 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: 0.7980 chunk 100 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 0.0770 chunk 24 optimal weight: 5.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- 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** N 82 GLN R 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8441 Z= 0.165 Angle : 0.487 8.528 11432 Z= 0.249 Chirality : 0.041 0.136 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.119 26.131 1158 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.35 % Allowed : 19.02 % Favored : 78.64 % 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: 1.28 (0.27), residues: 1033 helix: 2.64 (0.26), residues: 404 sheet: -0.22 (0.35), residues: 208 loop : -0.32 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 89 HIS 0.004 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 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 146 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 0.899 Fit side-chains REVERT: A 34 GLU cc_start: 0.7139 (tt0) cc_final: 0.6903 (mt-10) REVERT: A 132 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7861 (ttm110) REVERT: B 19 ARG cc_start: 0.7956 (ttp-110) cc_final: 0.7726 (ttp-110) REVERT: G 21 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8087 (mpp) REVERT: N 3 GLN cc_start: 0.8169 (pt0) cc_final: 0.7611 (pt0) REVERT: R 83 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.5949 (ttm170) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 1.1352 time to fit residues: 164.5724 Evaluate side-chains 139 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 49 SER 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 225 SER Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** R 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107098 restraints weight = 9726.353| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.42 r_work: 0.3135 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8441 Z= 0.335 Angle : 0.570 8.555 11432 Z= 0.295 Chirality : 0.045 0.139 1275 Planarity : 0.004 0.038 1456 Dihedral : 4.538 26.877 1158 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.68 % Allowed : 19.02 % 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: 1.05 (0.27), residues: 1033 helix: 2.45 (0.26), residues: 399 sheet: -0.31 (0.35), residues: 208 loop : -0.46 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 310 HIS 0.006 0.001 HIS A 209 PHE 0.018 0.002 PHE R 91 TYR 0.014 0.002 TYR R 304 ARG 0.004 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3492.40 seconds wall clock time: 62 minutes 3.19 seconds (3723.19 seconds total)