Starting phenix.real_space_refine on Wed Feb 14 01:47:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8m_24897/02_2024/7s8m_24897.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8m_24897/02_2024/7s8m_24897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8m_24897/02_2024/7s8m_24897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8m_24897/02_2024/7s8m_24897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8m_24897/02_2024/7s8m_24897.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8m_24897/02_2024/7s8m_24897.pdb" } resolution = 2.54 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5343 2.51 5 N 1408 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 15": "NH1" <-> "NH2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 206": "NH1" <-> "NH2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8346 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1707 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2564 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 401 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1743 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1892 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 39 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 4.84, per 1000 atoms: 0.58 Number of scatterers: 8346 At special positions: 0 Unit cell: (102.08, 117.92, 117.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1532 8.00 N 1408 7.00 C 5343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " 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: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 36.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.667A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 281 removed outlier: 4.144A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.541A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.683A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 removed outlier: 3.633A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 24 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.501A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.823A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.966A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY R 44 " --> pdb=" O ILE R 40 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE R 57 " --> pdb=" O TRP R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 95 removed outlier: 3.779A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 133 removed outlier: 3.874A pdb=" N THR R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 167 Processing helix chain 'R' and resid 177 through 212 Processing helix chain 'R' and resid 217 through 236 Processing helix chain 'R' and resid 236 through 250 removed outlier: 4.291A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TRP R 248 " --> pdb=" O PHE R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 190 Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.293A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.826A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.908A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.585A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.992A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.522A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.554A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.338A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2666 1.34 - 1.46: 1967 1.46 - 1.58: 3802 1.58 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 8522 Sorted by residual: bond pdb=" CB ASP R 75 " pdb=" CG ASP R 75 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.37e+00 bond pdb=" CG1 ILE C 58 " pdb=" CD1 ILE C 58 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.22e+00 bond pdb=" CG LEU R 237 " pdb=" CD1 LEU R 237 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.02e+00 bond pdb=" C GLU E 222 " pdb=" N TYR E 223 " ideal model delta sigma weight residual 1.330 1.318 0.012 1.47e-02 4.63e+03 7.05e-01 bond pdb=" CG LEU R 45 " pdb=" CD2 LEU R 45 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.66e-01 ... (remaining 8517 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.06: 132 106.06 - 113.04: 4674 113.04 - 120.03: 2818 120.03 - 127.02: 3849 127.02 - 134.01: 100 Bond angle restraints: 11573 Sorted by residual: angle pdb=" N PRO E 224 " pdb=" CA PRO E 224 " pdb=" C PRO E 224 " ideal model delta sigma weight residual 112.10 118.27 -6.17 2.60e+00 1.48e-01 5.64e+00 angle pdb=" N GLY B 352 " pdb=" CA GLY B 352 " pdb=" C GLY B 352 " ideal model delta sigma weight residual 114.67 117.97 -3.30 1.41e+00 5.03e-01 5.47e+00 angle pdb=" N ASP C 291 " pdb=" CA ASP C 291 " pdb=" C ASP C 291 " ideal model delta sigma weight residual 112.97 110.60 2.37 1.06e+00 8.90e-01 5.01e+00 angle pdb=" CA TYR E 178 " pdb=" CB TYR E 178 " pdb=" CG TYR E 178 " ideal model delta sigma weight residual 113.90 117.79 -3.89 1.80e+00 3.09e-01 4.66e+00 angle pdb=" CA ARG E 206 " pdb=" CB ARG E 206 " pdb=" CG ARG E 206 " ideal model delta sigma weight residual 114.10 118.19 -4.09 2.00e+00 2.50e-01 4.19e+00 ... (remaining 11568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 4587 16.95 - 33.89: 316 33.89 - 50.84: 68 50.84 - 67.78: 11 67.78 - 84.73: 5 Dihedral angle restraints: 4987 sinusoidal: 1808 harmonic: 3179 Sorted by residual: dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual -180.00 -154.06 -25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASN B 347 " pdb=" C ASN B 347 " pdb=" N LEU B 348 " pdb=" CA LEU B 348 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 4984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 838 0.033 - 0.066: 344 0.066 - 0.099: 105 0.099 - 0.133: 49 0.133 - 0.166: 8 Chirality restraints: 1344 Sorted by residual: chirality pdb=" CA TYR E 178 " pdb=" N TYR E 178 " pdb=" C TYR E 178 " pdb=" CB TYR E 178 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA PRO E 224 " pdb=" N PRO E 224 " pdb=" C PRO E 224 " pdb=" CB PRO E 224 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 1341 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 129 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C LEU R 129 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU R 129 " -0.011 2.00e-02 2.50e+03 pdb=" N SER R 130 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 242 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C GLN R 242 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN R 242 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP R 243 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 123 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C VAL R 123 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL R 123 " -0.010 2.00e-02 2.50e+03 pdb=" N SER R 124 " -0.009 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 268 2.72 - 3.26: 8118 3.26 - 3.81: 13659 3.81 - 4.35: 16864 4.35 - 4.90: 29665 Nonbonded interactions: 68574 Sorted by model distance: nonbonded pdb=" OE2 GLU B 14 " pdb=" OG1 THR E 57 " model vdw 2.171 2.440 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.200 2.440 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.207 2.440 nonbonded pdb=" O CYS B 254 " pdb=" NZ LYS B 317 " model vdw 2.241 2.520 nonbonded pdb=" OD1 ASP B 272 " pdb=" N LEU B 273 " model vdw 2.249 2.520 ... (remaining 68569 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.320 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.150 Find NCS groups from input model: 0.260 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:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 0.043 8522 Z= 0.240 Angle : 0.589 7.037 11573 Z= 0.326 Chirality : 0.043 0.166 1344 Planarity : 0.004 0.031 1452 Dihedral : 12.635 84.726 2932 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.46 (0.26), residues: 1082 helix: 2.00 (0.28), residues: 369 sheet: 0.15 (0.29), residues: 276 loop : -1.08 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.004 0.001 HIS C 142 PHE 0.019 0.002 PHE B 189 TYR 0.018 0.002 TYR E 178 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7754 (mmtp) cc_final: 0.7523 (mmtp) REVERT: C 25 CYS cc_start: 0.7535 (p) cc_final: 0.7145 (p) REVERT: C 254 ASP cc_start: 0.7040 (t70) cc_final: 0.6791 (t0) REVERT: R 109 MET cc_start: 0.6736 (ttp) cc_final: 0.6462 (ttm) REVERT: R 280 PHE cc_start: 0.7849 (t80) cc_final: 0.7147 (t80) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.8803 time to fit residues: 190.5368 Evaluate side-chains 183 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8522 Z= 0.281 Angle : 0.566 8.234 11573 Z= 0.296 Chirality : 0.043 0.156 1344 Planarity : 0.004 0.032 1452 Dihedral : 4.530 25.343 1173 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.60 % Allowed : 7.78 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.90 (0.26), residues: 1082 helix: 2.61 (0.28), residues: 373 sheet: 0.30 (0.29), residues: 276 loop : -1.04 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 190 HIS 0.004 0.001 HIS C 142 PHE 0.019 0.002 PHE B 189 TYR 0.022 0.002 TYR E 178 ARG 0.003 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 188 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7704 (mmtp) cc_final: 0.7494 (mmtp) REVERT: B 279 LYS cc_start: 0.8502 (mtmm) cc_final: 0.8172 (mtmm) REVERT: C 25 CYS cc_start: 0.7548 (p) cc_final: 0.7157 (p) REVERT: C 197 ARG cc_start: 0.6837 (mmt180) cc_final: 0.6595 (mmt180) REVERT: C 254 ASP cc_start: 0.7058 (t70) cc_final: 0.6810 (t70) REVERT: R 45 LEU cc_start: 0.7584 (mm) cc_final: 0.7175 (mm) REVERT: R 109 MET cc_start: 0.6614 (ttp) cc_final: 0.6305 (ttp) REVERT: R 280 PHE cc_start: 0.7903 (t80) cc_final: 0.7426 (t80) outliers start: 14 outliers final: 10 residues processed: 192 average time/residue: 0.9143 time to fit residues: 189.8039 Evaluate side-chains 189 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 0.0980 chunk 33 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN R 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8522 Z= 0.251 Angle : 0.541 7.298 11573 Z= 0.283 Chirality : 0.043 0.157 1344 Planarity : 0.003 0.032 1452 Dihedral : 4.425 25.117 1173 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.63 % Allowed : 10.30 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1082 helix: 2.79 (0.28), residues: 373 sheet: 0.31 (0.29), residues: 278 loop : -1.01 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.002 PHE B 189 TYR 0.019 0.002 TYR E 178 ARG 0.003 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7725 (mmtp) cc_final: 0.7515 (mmtp) REVERT: B 279 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8167 (mtmm) REVERT: C 25 CYS cc_start: 0.7539 (p) cc_final: 0.7124 (p) REVERT: C 197 ARG cc_start: 0.6849 (mmt180) cc_final: 0.6604 (mmt180) REVERT: C 217 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7156 (pmm) REVERT: C 254 ASP cc_start: 0.7048 (t70) cc_final: 0.6806 (t70) REVERT: C 258 ASP cc_start: 0.7072 (t0) cc_final: 0.6782 (t0) REVERT: R 45 LEU cc_start: 0.7597 (mm) cc_final: 0.7213 (mm) REVERT: R 109 MET cc_start: 0.6641 (ttp) cc_final: 0.6345 (ttp) REVERT: R 280 PHE cc_start: 0.7919 (t80) cc_final: 0.7469 (t80) outliers start: 23 outliers final: 13 residues processed: 199 average time/residue: 0.9438 time to fit residues: 202.8693 Evaluate side-chains 196 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 182 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN R 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8522 Z= 0.205 Angle : 0.512 6.378 11573 Z= 0.269 Chirality : 0.042 0.150 1344 Planarity : 0.003 0.033 1452 Dihedral : 4.270 23.143 1173 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.63 % Allowed : 12.13 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1082 helix: 2.83 (0.28), residues: 375 sheet: 0.27 (0.30), residues: 276 loop : -0.93 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE B 189 TYR 0.016 0.001 TYR E 178 ARG 0.002 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7712 (mmtp) cc_final: 0.7512 (mmtp) REVERT: B 279 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8169 (mtmm) REVERT: C 25 CYS cc_start: 0.7574 (p) cc_final: 0.7139 (p) REVERT: C 197 ARG cc_start: 0.6848 (mmt180) cc_final: 0.6588 (mmt180) REVERT: C 217 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7177 (pmm) REVERT: C 254 ASP cc_start: 0.7043 (t70) cc_final: 0.6807 (t70) REVERT: C 258 ASP cc_start: 0.7068 (t0) cc_final: 0.6785 (t0) REVERT: R 45 LEU cc_start: 0.7579 (mm) cc_final: 0.7219 (mm) REVERT: R 109 MET cc_start: 0.6579 (ttp) cc_final: 0.6345 (ttm) REVERT: R 280 PHE cc_start: 0.7920 (t80) cc_final: 0.7474 (t80) outliers start: 23 outliers final: 13 residues processed: 193 average time/residue: 0.9080 time to fit residues: 189.3774 Evaluate side-chains 195 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 71 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS C 268 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8522 Z= 0.222 Angle : 0.526 9.534 11573 Z= 0.274 Chirality : 0.042 0.151 1344 Planarity : 0.003 0.033 1452 Dihedral : 4.256 23.085 1173 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.86 % Allowed : 12.81 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1082 helix: 2.84 (0.28), residues: 375 sheet: 0.34 (0.30), residues: 278 loop : -0.92 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE B 189 TYR 0.018 0.002 TYR E 178 ARG 0.002 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7711 (mmtp) cc_final: 0.7500 (mmtp) REVERT: B 279 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8168 (mtmm) REVERT: C 25 CYS cc_start: 0.7559 (p) cc_final: 0.7122 (p) REVERT: C 254 ASP cc_start: 0.7044 (t70) cc_final: 0.6804 (t70) REVERT: C 258 ASP cc_start: 0.7063 (t0) cc_final: 0.6725 (t0) REVERT: R 45 LEU cc_start: 0.7600 (mm) cc_final: 0.7236 (mm) REVERT: R 109 MET cc_start: 0.6583 (ttp) cc_final: 0.6330 (ttp) REVERT: R 280 PHE cc_start: 0.7924 (t80) cc_final: 0.7483 (t80) outliers start: 25 outliers final: 20 residues processed: 191 average time/residue: 0.9124 time to fit residues: 188.5461 Evaluate side-chains 197 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.0000 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN R 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8522 Z= 0.217 Angle : 0.523 8.631 11573 Z= 0.273 Chirality : 0.042 0.150 1344 Planarity : 0.003 0.033 1452 Dihedral : 4.232 22.907 1173 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.32 % Allowed : 13.96 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1082 helix: 2.98 (0.27), residues: 369 sheet: 0.40 (0.30), residues: 273 loop : -0.88 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE B 189 TYR 0.017 0.002 TYR E 178 ARG 0.005 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7710 (mmtp) cc_final: 0.7491 (mmtp) REVERT: C 25 CYS cc_start: 0.7552 (p) cc_final: 0.7122 (p) REVERT: C 254 ASP cc_start: 0.7045 (t70) cc_final: 0.6793 (t70) REVERT: E 167 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: R 45 LEU cc_start: 0.7599 (mm) cc_final: 0.7245 (mm) REVERT: R 109 MET cc_start: 0.6579 (ttp) cc_final: 0.6341 (ttm) REVERT: R 280 PHE cc_start: 0.7927 (t80) cc_final: 0.7443 (t80) outliers start: 29 outliers final: 24 residues processed: 197 average time/residue: 0.8992 time to fit residues: 191.5222 Evaluate side-chains 201 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.0570 chunk 103 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN E 130 GLN R 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8522 Z= 0.179 Angle : 0.511 8.947 11573 Z= 0.265 Chirality : 0.041 0.149 1344 Planarity : 0.003 0.031 1452 Dihedral : 4.120 21.561 1173 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.86 % Allowed : 14.65 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1082 helix: 3.04 (0.27), residues: 369 sheet: 0.43 (0.30), residues: 276 loop : -0.83 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE B 189 TYR 0.015 0.001 TYR E 178 ARG 0.002 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7689 (mmtp) cc_final: 0.7487 (mmtp) REVERT: C 25 CYS cc_start: 0.7552 (p) cc_final: 0.7128 (p) REVERT: C 254 ASP cc_start: 0.7027 (t70) cc_final: 0.6773 (t70) REVERT: E 30 SER cc_start: 0.7779 (m) cc_final: 0.7530 (t) REVERT: R 45 LEU cc_start: 0.7593 (mm) cc_final: 0.7259 (mm) REVERT: R 109 MET cc_start: 0.6543 (ttp) cc_final: 0.6330 (ttm) REVERT: R 280 PHE cc_start: 0.7923 (t80) cc_final: 0.7447 (t80) outliers start: 25 outliers final: 21 residues processed: 189 average time/residue: 0.9347 time to fit residues: 190.8676 Evaluate side-chains 199 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 98 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN E 130 GLN R 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8522 Z= 0.207 Angle : 0.526 9.062 11573 Z= 0.272 Chirality : 0.042 0.149 1344 Planarity : 0.003 0.030 1452 Dihedral : 4.146 21.849 1173 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.86 % Allowed : 14.53 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.29 (0.26), residues: 1082 helix: 3.03 (0.27), residues: 369 sheet: 0.40 (0.30), residues: 278 loop : -0.79 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE B 189 TYR 0.017 0.002 TYR E 178 ARG 0.002 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7692 (mmtp) cc_final: 0.7489 (mmtp) REVERT: B 190 THR cc_start: 0.8595 (m) cc_final: 0.8382 (m) REVERT: C 25 CYS cc_start: 0.7561 (p) cc_final: 0.7150 (p) REVERT: C 254 ASP cc_start: 0.7036 (t70) cc_final: 0.6784 (t70) REVERT: E 30 SER cc_start: 0.7786 (m) cc_final: 0.7525 (t) REVERT: R 45 LEU cc_start: 0.7599 (mm) cc_final: 0.7238 (mm) REVERT: R 109 MET cc_start: 0.6565 (ttp) cc_final: 0.6330 (ttm) REVERT: R 280 PHE cc_start: 0.7925 (t80) cc_final: 0.7453 (t80) outliers start: 25 outliers final: 21 residues processed: 186 average time/residue: 0.9582 time to fit residues: 192.3195 Evaluate side-chains 197 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.1980 chunk 96 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN E 130 GLN R 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8522 Z= 0.227 Angle : 0.536 9.089 11573 Z= 0.278 Chirality : 0.042 0.152 1344 Planarity : 0.003 0.031 1452 Dihedral : 4.183 22.460 1173 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.75 % Allowed : 15.10 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.30 (0.26), residues: 1082 helix: 3.01 (0.27), residues: 369 sheet: 0.46 (0.31), residues: 273 loop : -0.77 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.001 PHE B 189 TYR 0.018 0.002 TYR E 178 ARG 0.002 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7720 (mmtp) cc_final: 0.7503 (mmtp) REVERT: B 190 THR cc_start: 0.8616 (m) cc_final: 0.8410 (m) REVERT: C 25 CYS cc_start: 0.7558 (p) cc_final: 0.7147 (p) REVERT: C 254 ASP cc_start: 0.7044 (t70) cc_final: 0.6791 (t70) REVERT: E 167 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: R 45 LEU cc_start: 0.7607 (mm) cc_final: 0.7241 (mm) REVERT: R 109 MET cc_start: 0.6590 (ttp) cc_final: 0.6339 (ttm) outliers start: 24 outliers final: 21 residues processed: 186 average time/residue: 0.9714 time to fit residues: 194.8039 Evaluate side-chains 195 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN E 130 GLN R 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8522 Z= 0.263 Angle : 0.560 11.701 11573 Z= 0.289 Chirality : 0.043 0.156 1344 Planarity : 0.003 0.031 1452 Dihedral : 4.280 23.554 1173 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.75 % Allowed : 15.33 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1082 helix: 2.93 (0.27), residues: 369 sheet: 0.52 (0.31), residues: 267 loop : -0.81 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.002 PHE B 189 TYR 0.020 0.002 TYR E 178 ARG 0.003 0.000 ARG R 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7729 (mmtp) cc_final: 0.7509 (mmtp) REVERT: B 243 MET cc_start: 0.8423 (tpt) cc_final: 0.8183 (tpt) REVERT: C 25 CYS cc_start: 0.7547 (p) cc_final: 0.7136 (p) REVERT: C 254 ASP cc_start: 0.7053 (t70) cc_final: 0.6806 (t70) REVERT: E 167 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: R 45 LEU cc_start: 0.7592 (mm) cc_final: 0.7200 (mm) REVERT: R 109 MET cc_start: 0.6600 (ttp) cc_final: 0.6287 (ttp) REVERT: R 280 PHE cc_start: 0.7821 (t80) cc_final: 0.7519 (t80) outliers start: 24 outliers final: 22 residues processed: 192 average time/residue: 0.9887 time to fit residues: 206.1022 Evaluate side-chains 200 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.0670 chunk 85 optimal weight: 0.0170 chunk 35 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 74 optimal weight: 0.0970 chunk 4 optimal weight: 0.3980 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN C 268 ASN E 130 GLN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.134106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119736 restraints weight = 11034.339| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.62 r_work: 0.3542 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8522 Z= 0.135 Angle : 0.492 8.516 11573 Z= 0.257 Chirality : 0.040 0.137 1344 Planarity : 0.003 0.030 1452 Dihedral : 3.983 19.249 1173 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.40 % Allowed : 15.79 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.36 (0.27), residues: 1082 helix: 3.09 (0.27), residues: 369 sheet: 0.39 (0.31), residues: 272 loop : -0.70 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.016 0.001 PHE R 280 TYR 0.010 0.001 TYR C 59 ARG 0.001 0.000 ARG R 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3762.15 seconds wall clock time: 67 minutes 31.56 seconds (4051.56 seconds total)