Starting phenix.real_space_refine on Fri Nov 15 09:23:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/11_2024/8id6_35358.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/11_2024/8id6_35358.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/8id6_35358/11_2024/8id6_35358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/11_2024/8id6_35358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/11_2024/8id6_35358.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id6_35358/11_2024/8id6_35358.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= 0.016 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 56 5.16 5 C 5596 2.51 5 N 1478 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8727 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2206 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 12, 'TRANS': 277} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2569 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 28 Chain: "Y" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 409 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1754 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.36, per 1000 atoms: 0.61 Number of scatterers: 8727 At special positions: 0 Unit cell: (106.47, 128.778, 115.596, 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 56 16.00 O 1597 8.00 N 1478 7.00 C 5596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 37.0% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'R' and resid 37 through 69 removed outlier: 3.983A pdb=" N THR R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL R 48 " --> pdb=" O THR R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 89 removed outlier: 3.676A pdb=" N ASN R 80 " --> pdb=" O CYS R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 101 removed outlier: 3.700A pdb=" N THR R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 114 Processing helix chain 'R' and resid 115 through 143 removed outlier: 3.656A pdb=" N LEU R 120 " --> pdb=" O TYR R 116 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 169 removed outlier: 3.738A pdb=" N ALA R 160 " --> pdb=" O ALA R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 removed outlier: 3.742A pdb=" N VAL R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE R 176 " --> pdb=" O PRO R 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 171 through 176' Processing helix chain 'R' and resid 200 through 216 Processing helix chain 'R' and resid 216 through 244 removed outlier: 3.563A pdb=" N SER R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 290 removed outlier: 3.987A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 301 through 312 removed outlier: 3.605A pdb=" N TRP R 305 " --> pdb=" O SER R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 315 No H-bonds generated for 'chain 'R' and resid 313 through 315' Processing helix chain 'R' and resid 316 through 321 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.649A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) 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 241 through 255 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.684A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.574A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.079A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 24 removed outlier: 3.889A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.759A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 221 through 225 removed outlier: 3.974A pdb=" N VAL S 225 " --> pdb=" O ALA S 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 177 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.223A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.715A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.824A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.786A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.054A 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 152 removed outlier: 3.996A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.070A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.514A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.725A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.093A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 149 removed outlier: 3.614A pdb=" N GLY S 226 " --> pdb=" O LEU S 246 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU S 175 " --> pdb=" O TYR S 191 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR S 191 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP S 177 " --> pdb=" O LEU S 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 147 through 149 removed outlier: 3.614A pdb=" N GLY S 226 " --> pdb=" O LEU S 246 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR S 239 " --> pdb=" O GLN S 232 " (cutoff:3.500A) 446 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: 2.77 Time building geometry restraints manager: 2.93 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: 1480 1.32 - 1.45: 2392 1.45 - 1.57: 4952 1.57 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 8905 Sorted by residual: bond pdb=" C GLY R 151 " pdb=" N ARG R 152 " ideal model delta sigma weight residual 1.335 1.227 0.107 1.25e-02 6.40e+03 7.37e+01 bond pdb=" C ARG R 264 " pdb=" O ARG R 264 " ideal model delta sigma weight residual 1.237 1.198 0.038 1.16e-02 7.43e+03 1.09e+01 bond pdb=" N ARG R 152 " pdb=" CA ARG R 152 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.64e+00 bond pdb=" C ARG A 21 " pdb=" O ARG A 21 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.17e-02 7.31e+03 5.95e+00 bond pdb=" CA ARG R 264 " pdb=" C ARG R 264 " ideal model delta sigma weight residual 1.524 1.496 0.027 1.26e-02 6.30e+03 4.73e+00 ... (remaining 8900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 11746 1.65 - 3.30: 269 3.30 - 4.96: 47 4.96 - 6.61: 18 6.61 - 8.26: 7 Bond angle restraints: 12087 Sorted by residual: angle pdb=" N SER S 194 " pdb=" CA SER S 194 " pdb=" C SER S 194 " ideal model delta sigma weight residual 112.88 118.50 -5.62 1.29e+00 6.01e-01 1.89e+01 angle pdb=" N ASN S 195 " pdb=" CA ASN S 195 " pdb=" C ASN S 195 " ideal model delta sigma weight residual 108.52 115.14 -6.62 1.63e+00 3.76e-01 1.65e+01 angle pdb=" N MET S 193 " pdb=" CA MET S 193 " pdb=" C MET S 193 " ideal model delta sigma weight residual 110.80 119.06 -8.26 2.13e+00 2.20e-01 1.50e+01 angle pdb=" CA TYR R 247 " pdb=" CB TYR R 247 " pdb=" CG TYR R 247 " ideal model delta sigma weight residual 113.90 120.14 -6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" N ILE R 92 " pdb=" CA ILE R 92 " pdb=" C ILE R 92 " ideal model delta sigma weight residual 108.88 115.75 -6.87 2.16e+00 2.14e-01 1.01e+01 ... (remaining 12082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 4958 17.24 - 34.48: 236 34.48 - 51.72: 44 51.72 - 68.96: 15 68.96 - 86.21: 6 Dihedral angle restraints: 5259 sinusoidal: 1958 harmonic: 3301 Sorted by residual: dihedral pdb=" N MET S 193 " pdb=" C MET S 193 " pdb=" CA MET S 193 " pdb=" CB MET S 193 " ideal model delta harmonic sigma weight residual 122.80 132.18 -9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" C MET S 193 " pdb=" N MET S 193 " pdb=" CA MET S 193 " pdb=" CB MET S 193 " ideal model delta harmonic sigma weight residual -122.60 -131.70 9.10 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1308 0.087 - 0.174: 99 0.174 - 0.261: 5 0.261 - 0.348: 1 0.348 - 0.435: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA MET S 193 " pdb=" N MET S 193 " pdb=" C MET S 193 " pdb=" CB MET S 193 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA ARG S 192 " pdb=" N ARG S 192 " pdb=" C ARG S 192 " pdb=" CB ARG S 192 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA SER S 194 " pdb=" N SER S 194 " pdb=" C SER S 194 " pdb=" CB SER S 194 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1411 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR Y 52 " -0.067 5.00e-02 4.00e+02 9.92e-02 1.58e+01 pdb=" N PRO Y 53 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO Y 53 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO Y 53 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 151 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C GLY R 151 " 0.066 2.00e-02 2.50e+03 pdb=" O GLY R 151 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG R 152 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO S 107 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.036 5.00e-02 4.00e+02 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 319 2.72 - 3.27: 8498 3.27 - 3.81: 13918 3.81 - 4.36: 17756 4.36 - 4.90: 30337 Nonbonded interactions: 70828 Sorted by model distance: nonbonded pdb=" NH1 ARG R 238 " pdb=" OD1 ASP R 259 " model vdw 2.180 3.120 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" ND2 ASN A 331 " model vdw 2.286 3.120 ... (remaining 70823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.850 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.107 8905 Z= 0.235 Angle : 0.668 8.258 12087 Z= 0.370 Chirality : 0.048 0.435 1414 Planarity : 0.006 0.099 1515 Dihedral : 11.398 86.206 3118 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.86 (0.25), residues: 1119 helix: 1.10 (0.27), residues: 383 sheet: 1.33 (0.29), residues: 283 loop : -0.32 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.021 0.002 PHE A 189 TYR 0.017 0.002 TYR S 191 ARG 0.005 0.001 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: Y 21 MET cc_start: 0.6695 (mpp) cc_final: 0.6441 (ttp) outliers start: 0 outliers final: 1 residues processed: 137 average time/residue: 1.4788 time to fit residues: 214.3195 Evaluate side-chains 94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.0050 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 GLN ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN A 195 HIS B 44 GLN B 259 GLN B 340 ASN S 187 GLN S 195 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8905 Z= 0.244 Angle : 0.595 6.879 12087 Z= 0.310 Chirality : 0.044 0.159 1414 Planarity : 0.005 0.072 1515 Dihedral : 5.285 50.826 1235 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.39 % Allowed : 7.28 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1119 helix: 1.64 (0.27), residues: 384 sheet: 1.06 (0.29), residues: 294 loop : -0.34 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 207 HIS 0.006 0.002 HIS S 233 PHE 0.017 0.002 PHE B 199 TYR 0.019 0.002 TYR B 105 ARG 0.004 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.041 Fit side-chains REVERT: R 178 ARG cc_start: 0.5439 (mmt180) cc_final: 0.5219 (mmm160) REVERT: B 118 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7296 (p0) REVERT: B 197 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7196 (mmp-170) REVERT: Y 21 MET cc_start: 0.6737 (mpp) cc_final: 0.6441 (ttm) outliers start: 22 outliers final: 7 residues processed: 102 average time/residue: 1.4582 time to fit residues: 157.4723 Evaluate side-chains 95 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 0.0770 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.0170 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 80 ASN ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN A 195 HIS B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8905 Z= 0.214 Angle : 0.548 7.011 12087 Z= 0.287 Chirality : 0.043 0.149 1414 Planarity : 0.005 0.072 1515 Dihedral : 5.104 50.809 1235 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.07 % Allowed : 8.70 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.15 (0.25), residues: 1119 helix: 1.84 (0.28), residues: 390 sheet: 1.07 (0.29), residues: 287 loop : -0.39 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS B 62 PHE 0.015 0.002 PHE B 151 TYR 0.015 0.002 TYR S 191 ARG 0.004 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8339 (mp) cc_final: 0.7719 (tt) REVERT: R 316 LEU cc_start: 0.5990 (mt) cc_final: 0.5733 (mm) REVERT: A 208 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7478 (ttp-110) REVERT: B 118 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7315 (p0) REVERT: Y 21 MET cc_start: 0.7117 (mpp) cc_final: 0.6628 (ttt) outliers start: 19 outliers final: 9 residues processed: 102 average time/residue: 1.4293 time to fit residues: 154.6531 Evaluate side-chains 96 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8905 Z= 0.276 Angle : 0.565 7.347 12087 Z= 0.296 Chirality : 0.044 0.164 1414 Planarity : 0.005 0.076 1515 Dihedral : 5.112 51.025 1235 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.07 % Allowed : 9.78 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1119 helix: 1.89 (0.27), residues: 387 sheet: 0.93 (0.29), residues: 290 loop : -0.57 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.007 0.001 HIS B 62 PHE 0.016 0.002 PHE B 278 TYR 0.015 0.002 TYR S 191 ARG 0.004 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: R 178 ARG cc_start: 0.5500 (mmt180) cc_final: 0.5260 (mmm160) REVERT: R 214 LEU cc_start: 0.8394 (mp) cc_final: 0.7782 (tt) REVERT: B 118 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7288 (p0) REVERT: Y 21 MET cc_start: 0.7327 (mpp) cc_final: 0.6690 (ttt) outliers start: 19 outliers final: 13 residues processed: 95 average time/residue: 1.4652 time to fit residues: 147.4672 Evaluate side-chains 94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.0670 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8905 Z= 0.189 Angle : 0.519 6.854 12087 Z= 0.270 Chirality : 0.041 0.141 1414 Planarity : 0.004 0.070 1515 Dihedral : 4.899 46.521 1235 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.04 % Allowed : 10.11 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.18 (0.25), residues: 1119 helix: 2.13 (0.27), residues: 388 sheet: 0.87 (0.29), residues: 292 loop : -0.49 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR S 191 ARG 0.003 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8396 (mp) cc_final: 0.7818 (tt) REVERT: R 316 LEU cc_start: 0.6174 (mt) cc_final: 0.5903 (mm) REVERT: B 118 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7237 (p0) REVERT: Y 21 MET cc_start: 0.7313 (mpp) cc_final: 0.6690 (ttt) outliers start: 28 outliers final: 14 residues processed: 97 average time/residue: 1.2256 time to fit residues: 126.1974 Evaluate side-chains 95 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL 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 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.0030 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN B 239 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8905 Z= 0.128 Angle : 0.473 6.864 12087 Z= 0.248 Chirality : 0.040 0.143 1414 Planarity : 0.004 0.060 1515 Dihedral : 4.581 43.763 1235 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.63 % Allowed : 11.85 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.44 (0.25), residues: 1119 helix: 2.40 (0.27), residues: 390 sheet: 0.95 (0.29), residues: 286 loop : -0.34 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR S 191 ARG 0.002 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 113 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5639 (tp) REVERT: R 214 LEU cc_start: 0.8390 (mp) cc_final: 0.7811 (tt) REVERT: R 316 LEU cc_start: 0.6071 (mt) cc_final: 0.5799 (mm) REVERT: B 118 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7231 (p0) REVERT: Y 21 MET cc_start: 0.7255 (mpp) cc_final: 0.6654 (ttt) outliers start: 15 outliers final: 9 residues processed: 96 average time/residue: 1.3731 time to fit residues: 140.3944 Evaluate side-chains 93 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 0.0870 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8905 Z= 0.154 Angle : 0.496 7.292 12087 Z= 0.257 Chirality : 0.040 0.142 1414 Planarity : 0.004 0.061 1515 Dihedral : 4.510 43.788 1235 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.28 % Allowed : 11.52 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.48 (0.25), residues: 1119 helix: 2.47 (0.27), residues: 390 sheet: 0.93 (0.29), residues: 286 loop : -0.33 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.013 0.001 TYR S 191 ARG 0.006 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8384 (mp) cc_final: 0.7822 (tt) REVERT: R 316 LEU cc_start: 0.6022 (mt) cc_final: 0.5769 (mm) REVERT: B 118 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7274 (p0) REVERT: Y 21 MET cc_start: 0.7253 (mpp) cc_final: 0.6656 (ttt) outliers start: 21 outliers final: 11 residues processed: 94 average time/residue: 1.4743 time to fit residues: 147.5440 Evaluate side-chains 93 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN B 155 ASN B 239 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8905 Z= 0.270 Angle : 0.555 6.725 12087 Z= 0.291 Chirality : 0.043 0.160 1414 Planarity : 0.005 0.073 1515 Dihedral : 4.730 43.280 1235 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.39 % Allowed : 11.96 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.26 (0.25), residues: 1119 helix: 2.37 (0.27), residues: 388 sheet: 0.86 (0.29), residues: 285 loop : -0.56 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.014 0.002 PHE B 278 TYR 0.012 0.002 TYR S 191 ARG 0.006 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8422 (mp) cc_final: 0.7827 (tt) REVERT: R 316 LEU cc_start: 0.6335 (mt) cc_final: 0.6070 (mm) REVERT: B 118 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7255 (p0) REVERT: Y 21 MET cc_start: 0.7157 (mpp) cc_final: 0.6518 (ttt) outliers start: 22 outliers final: 14 residues processed: 99 average time/residue: 1.4340 time to fit residues: 150.4605 Evaluate side-chains 97 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL 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 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.0060 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN A 22 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8905 Z= 0.142 Angle : 0.499 10.421 12087 Z= 0.256 Chirality : 0.040 0.136 1414 Planarity : 0.004 0.063 1515 Dihedral : 4.417 44.255 1235 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.63 % Allowed : 12.83 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.51 (0.25), residues: 1119 helix: 2.63 (0.27), residues: 388 sheet: 0.84 (0.29), residues: 286 loop : -0.35 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.012 0.001 TYR S 191 ARG 0.005 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8446 (mp) cc_final: 0.7880 (tt) REVERT: R 316 LEU cc_start: 0.6112 (mt) cc_final: 0.5860 (mm) REVERT: B 118 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7176 (p0) REVERT: Y 21 MET cc_start: 0.7063 (mpp) cc_final: 0.6407 (ttt) outliers start: 15 outliers final: 11 residues processed: 96 average time/residue: 1.4239 time to fit residues: 145.3293 Evaluate side-chains 96 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL 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 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8905 Z= 0.159 Angle : 0.505 8.052 12087 Z= 0.263 Chirality : 0.041 0.137 1414 Planarity : 0.004 0.061 1515 Dihedral : 4.401 44.584 1235 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.41 % Allowed : 13.04 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.51 (0.25), residues: 1119 helix: 2.68 (0.27), residues: 387 sheet: 0.83 (0.29), residues: 286 loop : -0.38 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.012 0.001 PHE B 234 TYR 0.016 0.001 TYR B 59 ARG 0.006 0.000 ARG R 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8452 (mp) cc_final: 0.7884 (tt) REVERT: R 316 LEU cc_start: 0.6191 (mt) cc_final: 0.5941 (mm) REVERT: B 118 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7203 (p0) REVERT: Y 21 MET cc_start: 0.6996 (mpp) cc_final: 0.6326 (ttt) outliers start: 13 outliers final: 12 residues processed: 92 average time/residue: 1.4276 time to fit residues: 139.2975 Evaluate side-chains 94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL 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 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.193231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128112 restraints weight = 9240.928| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.07 r_work: 0.3014 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8905 Z= 0.289 Angle : 0.587 10.460 12087 Z= 0.304 Chirality : 0.044 0.164 1414 Planarity : 0.005 0.074 1515 Dihedral : 4.689 44.253 1235 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.85 % Allowed : 12.72 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.26 (0.25), residues: 1119 helix: 2.55 (0.27), residues: 381 sheet: 0.73 (0.29), residues: 275 loop : -0.56 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.017 0.002 PHE B 234 TYR 0.018 0.002 TYR B 59 ARG 0.006 0.001 ARG R 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3429.88 seconds wall clock time: 68 minutes 9.85 seconds (4089.85 seconds total)