Starting phenix.real_space_refine on Wed Feb 14 05:08:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/02_2024/7wj5_32543.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/02_2024/7wj5_32543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/02_2024/7wj5_32543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/02_2024/7wj5_32543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/02_2024/7wj5_32543.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wj5_32543/02_2024/7wj5_32543.pdb" } resolution = 3.72 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= 1.033 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 65 5.16 5 C 5551 2.51 5 N 1476 2.21 5 O 1568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8660 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1653 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2226 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 5.08, per 1000 atoms: 0.59 Number of scatterers: 8660 At special positions: 0 Unit cell: (106.112, 124.35, 117.718, 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 65 16.00 O 1568 8.00 N 1476 7.00 C 5551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS S 3 " - pdb=" SG CYS S 14 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 16 sheets defined 35.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.895A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.209A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.735A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.560A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 removed outlier: 3.776A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.902A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 72 through 75 removed outlier: 3.822A pdb=" N LYS R 75 " --> pdb=" O ALA R 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 72 through 75' Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 95 through 106 removed outlier: 4.283A pdb=" N LEU R 99 " --> pdb=" O GLY R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 146 Processing helix chain 'R' and resid 148 through 153 removed outlier: 4.055A pdb=" N LYS R 152 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 173 Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 202 through 217 removed outlier: 3.658A pdb=" N THR R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 237 Processing helix chain 'R' and resid 251 through 282 Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 287 through 315 removed outlier: 3.891A pdb=" N TYR R 302 " --> pdb=" O VAL R 298 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 9.613A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 9.613A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.652A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.649A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.090A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.569A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.572A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.791A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.685A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.270A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 147 Processing sheet with id=AB6, first strand: chain 'R' and resid 181 through 185 Processing sheet with id=AB7, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.544A pdb=" N PHE S 7 " --> pdb=" O THR S 10 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1242 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: 2.44 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2743 1.34 - 1.46: 2191 1.46 - 1.58: 3818 1.58 - 1.70: 0 1.70 - 1.81: 94 Bond restraints: 8846 Sorted by residual: bond pdb=" CA SER B 189 " pdb=" CB SER B 189 " ideal model delta sigma weight residual 1.535 1.516 0.019 1.90e-02 2.77e+03 1.02e+00 bond pdb=" CB PRO E 224 " pdb=" CG PRO E 224 " ideal model delta sigma weight residual 1.506 1.471 0.035 3.90e-02 6.57e+02 8.06e-01 bond pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 1.498 1.472 0.026 3.10e-02 1.04e+03 7.01e-01 bond pdb=" CG1 ILE R 209 " pdb=" CD1 ILE R 209 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.79e-01 bond pdb=" C ILE A 264 " pdb=" N ILE A 265 " ideal model delta sigma weight residual 1.327 1.304 0.023 2.97e-02 1.13e+03 5.99e-01 ... (remaining 8841 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.07: 151 106.07 - 113.07: 4858 113.07 - 120.06: 3015 120.06 - 127.06: 3874 127.06 - 134.06: 96 Bond angle restraints: 11994 Sorted by residual: angle pdb=" N LEU R 96 " pdb=" CA LEU R 96 " pdb=" C LEU R 96 " ideal model delta sigma weight residual 109.81 115.83 -6.02 2.21e+00 2.05e-01 7.42e+00 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 125.26 -8.96 3.50e+00 8.16e-02 6.55e+00 angle pdb=" C ARG R 241 " pdb=" N VAL R 242 " pdb=" CA VAL R 242 " ideal model delta sigma weight residual 121.97 126.42 -4.45 1.80e+00 3.09e-01 6.10e+00 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 124.90 -8.60 3.50e+00 8.16e-02 6.03e+00 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 113.65 110.08 3.57 1.47e+00 4.63e-01 5.91e+00 ... (remaining 11989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 4868 16.60 - 33.19: 297 33.19 - 49.79: 47 49.79 - 66.38: 7 66.38 - 82.98: 1 Dihedral angle restraints: 5220 sinusoidal: 1953 harmonic: 3267 Sorted by residual: dihedral pdb=" CA TYR A 320 " pdb=" C TYR A 320 " pdb=" N THR A 321 " pdb=" CA THR A 321 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 844 0.032 - 0.064: 374 0.064 - 0.096: 112 0.096 - 0.127: 46 0.127 - 0.159: 6 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1379 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO B 236 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 287 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO R 288 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 288 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 288 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 108 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO R 109 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO R 109 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 109 " 0.016 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 344 2.72 - 3.26: 8665 3.26 - 3.81: 14372 3.81 - 4.35: 17028 4.35 - 4.90: 30051 Nonbonded interactions: 70460 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.173 2.440 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.186 2.440 nonbonded pdb=" OH TYR A 320 " pdb=" O SER R 244 " model vdw 2.199 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.206 2.440 nonbonded pdb=" O LYS A 349 " pdb=" ND2 ASN R 318 " model vdw 2.244 2.520 ... (remaining 70455 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.010 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: 4.150 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.860 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.004 0.035 8846 Z= 0.237 Angle : 0.546 8.958 11994 Z= 0.288 Chirality : 0.041 0.159 1382 Planarity : 0.003 0.031 1495 Dihedral : 10.788 82.979 3102 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.05 % Allowed : 7.63 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1111 helix: 2.25 (0.28), residues: 349 sheet: 0.33 (0.30), residues: 283 loop : -0.19 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 107 PHE 0.012 0.001 PHE E 27 TYR 0.010 0.001 TYR R 211 ARG 0.002 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.6043 (mmt) cc_final: 0.5559 (mpp) REVERT: B 57 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7614 (mtpt) REVERT: B 59 TYR cc_start: 0.8299 (m-80) cc_final: 0.8076 (m-80) REVERT: B 75 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: B 76 ASP cc_start: 0.8563 (p0) cc_final: 0.8320 (p0) REVERT: B 234 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: B 267 ASP cc_start: 0.7322 (m-30) cc_final: 0.6784 (m-30) REVERT: R 51 PHE cc_start: 0.7190 (m-10) cc_final: 0.6873 (m-10) REVERT: R 180 TYR cc_start: 0.7496 (m-10) cc_final: 0.7110 (m-10) outliers start: 28 outliers final: 12 residues processed: 221 average time/residue: 0.2199 time to fit residues: 65.3284 Evaluate side-chains 189 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 220 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8846 Z= 0.180 Angle : 0.533 8.288 11994 Z= 0.277 Chirality : 0.041 0.147 1382 Planarity : 0.004 0.030 1495 Dihedral : 5.511 59.449 1238 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 3.38 % Allowed : 11.00 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.11 (0.26), residues: 1111 helix: 2.24 (0.28), residues: 350 sheet: 0.49 (0.30), residues: 276 loop : -0.18 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.010 0.001 PHE E 27 TYR 0.014 0.001 TYR E 178 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.6078 (mmt) cc_final: 0.5866 (tpp) REVERT: B 57 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7893 (mtpt) REVERT: B 59 TYR cc_start: 0.8275 (m-80) cc_final: 0.8022 (m-80) REVERT: B 75 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7488 (mt0) REVERT: B 76 ASP cc_start: 0.8554 (p0) cc_final: 0.8303 (p0) REVERT: B 234 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: B 267 ASP cc_start: 0.7335 (m-30) cc_final: 0.6798 (m-30) REVERT: R 51 PHE cc_start: 0.7184 (m-10) cc_final: 0.6912 (m-10) REVERT: R 180 TYR cc_start: 0.7239 (m-10) cc_final: 0.6931 (m-10) outliers start: 31 outliers final: 21 residues processed: 201 average time/residue: 0.2095 time to fit residues: 57.5172 Evaluate side-chains 191 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 18 GLN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8846 Z= 0.157 Angle : 0.514 7.620 11994 Z= 0.270 Chirality : 0.040 0.143 1382 Planarity : 0.003 0.030 1495 Dihedral : 5.367 58.850 1236 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.42 % Favored : 96.49 % Rotamer: Outliers : 4.14 % Allowed : 11.44 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.08 (0.26), residues: 1111 helix: 2.18 (0.28), residues: 350 sheet: 0.57 (0.30), residues: 260 loop : -0.22 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 211 HIS 0.002 0.001 HIS B 225 PHE 0.009 0.001 PHE A 189 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 1.055 Fit side-chains REVERT: A 243 MET cc_start: 0.6072 (mmt) cc_final: 0.5869 (tpp) REVERT: B 57 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7860 (mtpt) REVERT: B 59 TYR cc_start: 0.8265 (m-80) cc_final: 0.7986 (m-80) REVERT: B 75 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: B 76 ASP cc_start: 0.8573 (p0) cc_final: 0.8320 (p0) REVERT: B 234 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: R 51 PHE cc_start: 0.7197 (m-10) cc_final: 0.6926 (m-10) REVERT: R 178 MET cc_start: 0.6586 (ptp) cc_final: 0.5470 (tpp) REVERT: R 270 LEU cc_start: 0.8629 (tp) cc_final: 0.8306 (tp) outliers start: 38 outliers final: 22 residues processed: 195 average time/residue: 0.2186 time to fit residues: 58.1677 Evaluate side-chains 187 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 60 optimal weight: 0.0070 overall best weight: 0.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8846 Z= 0.161 Angle : 0.510 7.536 11994 Z= 0.267 Chirality : 0.040 0.149 1382 Planarity : 0.003 0.030 1495 Dihedral : 5.191 59.802 1229 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.47 % Allowed : 12.53 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.10 (0.26), residues: 1111 helix: 2.29 (0.28), residues: 343 sheet: 0.54 (0.30), residues: 260 loop : -0.21 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 197 HIS 0.002 0.001 HIS R 107 PHE 0.009 0.001 PHE A 189 TYR 0.011 0.001 TYR E 178 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 169 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.7718 (t80) cc_final: 0.7475 (t80) REVERT: A 243 MET cc_start: 0.6114 (mmt) cc_final: 0.5884 (tpp) REVERT: B 57 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7882 (mtpt) REVERT: B 59 TYR cc_start: 0.8229 (m-80) cc_final: 0.7960 (m-80) REVERT: B 75 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7483 (mt0) REVERT: B 76 ASP cc_start: 0.8558 (p0) cc_final: 0.8323 (p0) REVERT: B 188 MET cc_start: 0.7596 (mtm) cc_final: 0.7220 (mtt) REVERT: B 234 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: E 206 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7381 (ptp90) REVERT: R 51 PHE cc_start: 0.7171 (m-10) cc_final: 0.6878 (m-10) REVERT: R 153 TRP cc_start: 0.6018 (OUTLIER) cc_final: 0.5500 (m-10) REVERT: R 180 TYR cc_start: 0.7237 (m-10) cc_final: 0.6979 (m-10) REVERT: R 194 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7615 (t) REVERT: R 248 LYS cc_start: 0.6974 (mtmm) cc_final: 0.6723 (mptt) REVERT: R 270 LEU cc_start: 0.8648 (tp) cc_final: 0.8323 (tp) outliers start: 41 outliers final: 29 residues processed: 194 average time/residue: 0.2218 time to fit residues: 58.8092 Evaluate side-chains 194 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.0020 chunk 0 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8846 Z= 0.142 Angle : 0.498 7.316 11994 Z= 0.260 Chirality : 0.040 0.151 1382 Planarity : 0.003 0.028 1495 Dihedral : 5.073 58.497 1229 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.36 % Allowed : 13.40 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.08 (0.26), residues: 1111 helix: 2.13 (0.28), residues: 349 sheet: 0.58 (0.30), residues: 258 loop : -0.16 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 197 HIS 0.002 0.001 HIS R 107 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR E 178 ARG 0.003 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.7727 (t80) cc_final: 0.7509 (t80) REVERT: A 243 MET cc_start: 0.6154 (mmt) cc_final: 0.5928 (tpp) REVERT: B 59 TYR cc_start: 0.8219 (m-80) cc_final: 0.7960 (m-80) REVERT: B 75 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: B 76 ASP cc_start: 0.8528 (p0) cc_final: 0.8301 (p0) REVERT: B 234 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: C 40 TYR cc_start: 0.8210 (t80) cc_final: 0.7921 (t80) REVERT: E 206 ARG cc_start: 0.7637 (mtm110) cc_final: 0.7389 (ptp90) REVERT: R 51 PHE cc_start: 0.7156 (m-10) cc_final: 0.6846 (m-10) REVERT: R 153 TRP cc_start: 0.6028 (OUTLIER) cc_final: 0.5479 (m-10) REVERT: R 194 THR cc_start: 0.7751 (t) cc_final: 0.7478 (t) REVERT: R 248 LYS cc_start: 0.6948 (mtmm) cc_final: 0.6713 (mptt) REVERT: R 270 LEU cc_start: 0.8640 (tp) cc_final: 0.8372 (tp) outliers start: 40 outliers final: 28 residues processed: 196 average time/residue: 0.2235 time to fit residues: 59.1908 Evaluate side-chains 194 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 : 0.002 0.036 8846 Z= 0.160 Angle : 0.531 11.887 11994 Z= 0.271 Chirality : 0.040 0.159 1382 Planarity : 0.003 0.028 1495 Dihedral : 5.030 58.129 1228 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.47 % Allowed : 13.94 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.08 (0.26), residues: 1111 helix: 2.22 (0.28), residues: 342 sheet: 0.63 (0.31), residues: 249 loop : -0.22 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 197 HIS 0.002 0.001 HIS R 107 PHE 0.009 0.001 PHE A 189 TYR 0.010 0.001 TYR E 178 ARG 0.003 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 1.268 Fit side-chains REVERT: A 243 MET cc_start: 0.6142 (mmt) cc_final: 0.5931 (tpp) REVERT: B 59 TYR cc_start: 0.8261 (m-80) cc_final: 0.7938 (m-80) REVERT: B 75 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7476 (mt0) REVERT: B 76 ASP cc_start: 0.8535 (p0) cc_final: 0.8306 (p0) REVERT: B 234 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: C 40 TYR cc_start: 0.8222 (t80) cc_final: 0.7921 (t80) REVERT: E 206 ARG cc_start: 0.7633 (mtm110) cc_final: 0.7410 (ptp90) REVERT: R 74 MET cc_start: 0.5103 (ppp) cc_final: 0.4381 (ppp) REVERT: R 153 TRP cc_start: 0.6010 (OUTLIER) cc_final: 0.5437 (m-10) REVERT: R 194 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7454 (t) REVERT: R 248 LYS cc_start: 0.6905 (mtmm) cc_final: 0.6668 (mptt) REVERT: R 270 LEU cc_start: 0.8637 (tp) cc_final: 0.8327 (tp) outliers start: 41 outliers final: 34 residues processed: 195 average time/residue: 0.2581 time to fit residues: 68.2630 Evaluate side-chains 202 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.0050 chunk 32 optimal weight: 6.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8846 Z= 0.209 Angle : 0.555 11.178 11994 Z= 0.286 Chirality : 0.041 0.166 1382 Planarity : 0.003 0.029 1495 Dihedral : 5.157 57.843 1228 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.58 % Allowed : 14.71 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.06 (0.26), residues: 1111 helix: 2.21 (0.29), residues: 342 sheet: 0.60 (0.31), residues: 249 loop : -0.22 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 197 HIS 0.002 0.001 HIS R 107 PHE 0.010 0.001 PHE A 189 TYR 0.010 0.001 TYR R 180 ARG 0.003 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 0.979 Fit side-chains REVERT: A 243 MET cc_start: 0.6143 (mmt) cc_final: 0.5913 (tpp) REVERT: B 75 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7601 (mt0) REVERT: B 234 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: E 206 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7397 (ptp90) REVERT: R 74 MET cc_start: 0.5134 (ppp) cc_final: 0.4831 (ppp) REVERT: R 153 TRP cc_start: 0.5989 (OUTLIER) cc_final: 0.5414 (m-10) REVERT: R 194 THR cc_start: 0.7714 (OUTLIER) cc_final: 0.7403 (t) REVERT: R 248 LYS cc_start: 0.6872 (mtmm) cc_final: 0.6640 (mptt) outliers start: 42 outliers final: 33 residues processed: 191 average time/residue: 0.2161 time to fit residues: 56.1508 Evaluate side-chains 195 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8846 Z= 0.157 Angle : 0.528 10.816 11994 Z= 0.272 Chirality : 0.041 0.181 1382 Planarity : 0.003 0.028 1495 Dihedral : 5.069 59.431 1228 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.81 % Allowed : 15.80 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.08 (0.26), residues: 1111 helix: 2.24 (0.28), residues: 342 sheet: 0.59 (0.31), residues: 249 loop : -0.22 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 197 HIS 0.002 0.001 HIS R 107 PHE 0.010 0.001 PHE A 223 TYR 0.010 0.001 TYR E 178 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 0.918 Fit side-chains REVERT: A 243 MET cc_start: 0.6136 (mmt) cc_final: 0.5917 (tpp) REVERT: B 234 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: R 74 MET cc_start: 0.5145 (ppp) cc_final: 0.4885 (ppp) REVERT: R 153 TRP cc_start: 0.5979 (OUTLIER) cc_final: 0.5411 (m-10) REVERT: R 174 ILE cc_start: 0.8101 (pt) cc_final: 0.7811 (pt) REVERT: R 194 THR cc_start: 0.7632 (t) cc_final: 0.7399 (t) REVERT: R 248 LYS cc_start: 0.6797 (mtmm) cc_final: 0.6593 (mptt) REVERT: R 270 LEU cc_start: 0.8580 (tp) cc_final: 0.8276 (tp) REVERT: R 305 SER cc_start: 0.8015 (OUTLIER) cc_final: 0.7765 (t) outliers start: 35 outliers final: 31 residues processed: 190 average time/residue: 0.2148 time to fit residues: 55.6926 Evaluate side-chains 198 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.0670 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8846 Z= 0.145 Angle : 0.512 7.213 11994 Z= 0.267 Chirality : 0.040 0.173 1382 Planarity : 0.003 0.028 1495 Dihedral : 4.646 57.081 1225 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.49 % Allowed : 16.23 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.12 (0.26), residues: 1111 helix: 2.28 (0.28), residues: 342 sheet: 0.55 (0.31), residues: 258 loop : -0.17 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP R 197 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE A 223 TYR 0.011 0.001 TYR E 178 ARG 0.004 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.6158 (mmt) cc_final: 0.5923 (tpp) REVERT: B 234 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: C 40 TYR cc_start: 0.8209 (t80) cc_final: 0.7923 (t80) REVERT: R 74 MET cc_start: 0.5131 (ppp) cc_final: 0.4597 (ppp) REVERT: R 131 PHE cc_start: 0.6272 (m-80) cc_final: 0.5845 (m-80) REVERT: R 153 TRP cc_start: 0.6008 (OUTLIER) cc_final: 0.5425 (m-10) REVERT: R 174 ILE cc_start: 0.7855 (pt) cc_final: 0.7542 (pt) REVERT: R 270 LEU cc_start: 0.8611 (tp) cc_final: 0.8357 (tp) outliers start: 32 outliers final: 29 residues processed: 191 average time/residue: 0.2137 time to fit residues: 55.1361 Evaluate side-chains 196 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 88 optimal weight: 0.0270 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 0.0970 overall best weight: 1.1438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8846 Z= 0.180 Angle : 0.534 7.315 11994 Z= 0.278 Chirality : 0.041 0.183 1382 Planarity : 0.003 0.036 1495 Dihedral : 4.683 56.565 1224 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.38 % Allowed : 16.99 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.07 (0.26), residues: 1111 helix: 2.21 (0.28), residues: 342 sheet: 0.46 (0.31), residues: 264 loop : -0.14 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP R 197 HIS 0.004 0.001 HIS B 225 PHE 0.010 0.001 PHE A 189 TYR 0.009 0.001 TYR E 178 ARG 0.009 0.000 ARG E 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.6154 (mmt) cc_final: 0.5915 (tpp) REVERT: B 234 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: E 206 ARG cc_start: 0.7666 (mtm110) cc_final: 0.7200 (ptp90) REVERT: R 74 MET cc_start: 0.5143 (ppp) cc_final: 0.4601 (ppp) REVERT: R 131 PHE cc_start: 0.6396 (m-80) cc_final: 0.5889 (m-80) REVERT: R 153 TRP cc_start: 0.5995 (OUTLIER) cc_final: 0.5404 (m-10) outliers start: 31 outliers final: 29 residues processed: 183 average time/residue: 0.2083 time to fit residues: 52.6027 Evaluate side-chains 191 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 77 optimal weight: 0.0870 chunk 5 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.166224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126306 restraints weight = 11358.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.128193 restraints weight = 9612.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129663 restraints weight = 7562.871| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8846 Z= 0.291 Angle : 0.609 9.045 11994 Z= 0.316 Chirality : 0.043 0.169 1382 Planarity : 0.004 0.045 1495 Dihedral : 5.094 58.050 1224 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.81 % Allowed : 17.65 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.82 (0.26), residues: 1111 helix: 1.90 (0.28), residues: 348 sheet: 0.23 (0.30), residues: 276 loop : -0.18 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 197 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.002 PHE E 27 TYR 0.012 0.002 TYR R 273 ARG 0.007 0.000 ARG E 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.37 seconds wall clock time: 37 minutes 48.27 seconds (2268.27 seconds total)