Starting phenix.real_space_refine on Fri Mar 15 02:08:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/03_2024/8f2b_28812.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/03_2024/8f2b_28812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/03_2024/8f2b_28812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/03_2024/8f2b_28812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/03_2024/8f2b_28812.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2b_28812/03_2024/8f2b_28812.pdb" } resolution = 2.0 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= 0.006 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 74 5.16 5 C 6643 2.51 5 N 1740 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E ARG 140": "NH1" <-> "NH2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R GLU 255": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R GLU 332": "OE1" <-> "OE2" Residue "R GLU 334": "OE1" <-> "OE2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R ARG 404": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10360 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1876 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 420 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 817 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "P" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 278 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} Chain: "R" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3025 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 308 Unusual residues: {'NAG': 3, 'P42': 1, 'PLM': 8, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 5.59, per 1000 atoms: 0.54 Number of scatterers: 10360 At special positions: 0 Unit cell: (111.15, 99.45, 149.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 1 15.00 O 1902 8.00 N 1740 7.00 C 6643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 125 " " NAG R 503 " - " ASN R 130 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.42 Conformation dependent library (CDL) restraints added in 1.7 seconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 45.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.618A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.547A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.802A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.615A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.608A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.585A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.529A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.895A pdb=" N GLU E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) Proline residue: E 38 - end of helix removed outlier: 3.549A pdb=" N MET E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 51 " --> pdb=" O MET E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 61 Processing helix chain 'E' and resid 62 through 80 removed outlier: 3.668A pdb=" N MET E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 100 removed outlier: 3.788A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 141 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 131 through 135 removed outlier: 3.551A pdb=" N ASN R 135 " --> pdb=" O THR R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.533A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 204 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.613A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.614A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 268 Processing helix chain 'R' and resid 270 through 282 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.404A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.416A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.570A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.797A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.631A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.772A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.624A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.350A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.836A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'R' and resid 90 through 94 Processing sheet with id=AB5, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.580A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1446 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: 2.87 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1642 1.31 - 1.44: 2931 1.44 - 1.56: 5884 1.56 - 1.69: 2 1.69 - 1.81: 104 Bond restraints: 10563 Sorted by residual: bond pdb=" C02 D6M P 101 " pdb=" N03 D6M P 101 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C LYS P 21 " pdb=" O LYS P 21 " ideal model delta sigma weight residual 1.234 1.187 0.046 1.44e-02 4.82e+03 1.04e+01 bond pdb=" N VAL E 79 " pdb=" CA VAL E 79 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 9.98e+00 bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.185 0.062 2.00e-02 2.50e+03 9.65e+00 bond pdb=" N VAL E 80 " pdb=" CA VAL E 80 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.17e-02 7.31e+03 7.19e+00 ... (remaining 10558 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.84: 207 105.84 - 112.96: 5609 112.96 - 120.07: 3748 120.07 - 127.19: 4596 127.19 - 134.30: 128 Bond angle restraints: 14288 Sorted by residual: angle pdb=" N GLU E 76 " pdb=" CA GLU E 76 " pdb=" C GLU E 76 " ideal model delta sigma weight residual 111.07 106.17 4.90 1.07e+00 8.73e-01 2.10e+01 angle pdb=" CA TRP E 84 " pdb=" C TRP E 84 " pdb=" N PRO E 85 " ideal model delta sigma weight residual 118.23 121.65 -3.42 9.20e-01 1.18e+00 1.38e+01 angle pdb=" N GLU R 255 " pdb=" CA GLU R 255 " pdb=" C GLU R 255 " ideal model delta sigma weight residual 113.97 109.43 4.54 1.28e+00 6.10e-01 1.26e+01 angle pdb=" N VAL E 80 " pdb=" CA VAL E 80 " pdb=" C VAL E 80 " ideal model delta sigma weight residual 113.07 108.79 4.28 1.36e+00 5.41e-01 9.88e+00 angle pdb=" C ASN E 29 " pdb=" CA ASN E 29 " pdb=" CB ASN E 29 " ideal model delta sigma weight residual 110.19 105.06 5.13 1.64e+00 3.72e-01 9.78e+00 ... (remaining 14283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.30: 6094 24.30 - 48.60: 286 48.60 - 72.90: 57 72.90 - 97.20: 7 97.20 - 121.50: 4 Dihedral angle restraints: 6448 sinusoidal: 2739 harmonic: 3709 Sorted by residual: dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 141.79 -48.79 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 131.10 -38.10 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" CAI P42 R 512 " pdb=" CAJ P42 R 512 " pdb=" CAK P42 R 512 " pdb=" CAL P42 R 512 " ideal model delta sinusoidal sigma weight residual 179.92 58.42 121.50 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 6445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1270 0.050 - 0.100: 251 0.100 - 0.150: 47 0.150 - 0.200: 6 0.200 - 0.250: 3 Chirality restraints: 1577 Sorted by residual: chirality pdb=" CA TYR E 83 " pdb=" N TYR E 83 " pdb=" C TYR E 83 " pdb=" CB TYR E 83 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL E 79 " pdb=" CA VAL E 79 " pdb=" CG1 VAL E 79 " pdb=" CG2 VAL E 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASN E 29 " pdb=" N ASN E 29 " pdb=" C ASN E 29 " pdb=" CB ASN E 29 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1574 not shown) Planarity restraints: 1797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO B 236 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 37 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO E 38 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO G 55 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.019 5.00e-02 4.00e+02 ... (remaining 1794 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2808 2.80 - 3.33: 9321 3.33 - 3.85: 17500 3.85 - 4.38: 21502 4.38 - 4.90: 35815 Nonbonded interactions: 86946 Sorted by model distance: nonbonded pdb=" O SER A 352 " pdb=" OG SER A 352 " model vdw 2.278 2.440 nonbonded pdb=" O SER P 20 " pdb=" OG SER P 20 " model vdw 2.295 2.440 nonbonded pdb=" OE1 GLN R 227 " pdb=" O HOH R 601 " model vdw 2.303 2.440 nonbonded pdb=" OD2 ASP R 373 " pdb=" O HOH R 602 " model vdw 2.305 2.440 nonbonded pdb=" OE1 GLU R 240 " pdb=" O HOH R 603 " model vdw 2.312 2.440 ... (remaining 86941 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=0.00 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.540 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.340 Find NCS groups from input model: 0.280 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:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 0.112 10563 Z= 0.256 Angle : 0.554 7.057 14288 Z= 0.324 Chirality : 0.043 0.250 1577 Planarity : 0.003 0.039 1794 Dihedral : 14.226 121.499 4022 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.32 % Allowed : 12.56 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.02 (0.20), residues: 1255 helix: -1.84 (0.17), residues: 504 sheet: -0.17 (0.31), residues: 234 loop : -1.17 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.002 0.001 HIS A 387 PHE 0.010 0.001 PHE B 151 TYR 0.015 0.001 TYR E 83 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4201 (mmp) cc_final: 0.3710 (mpp) REVERT: R 261 TRP cc_start: 0.5889 (m100) cc_final: 0.5634 (m100) REVERT: R 327 MET cc_start: 0.7279 (mtm) cc_final: 0.6728 (mmm) REVERT: R 374 TYR cc_start: 0.6131 (m-80) cc_final: 0.5923 (m-80) outliers start: 14 outliers final: 1 residues processed: 215 average time/residue: 1.4220 time to fit residues: 325.0731 Evaluate side-chains 156 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 59 GLN A 294 GLN B 13 GLN B 155 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 93 GLN R 179 GLN R 186 ASN R 223 HIS R 257 GLN R 318 ASN R 408 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10563 Z= 0.215 Angle : 0.596 7.966 14288 Z= 0.319 Chirality : 0.043 0.145 1577 Planarity : 0.005 0.039 1794 Dihedral : 10.358 161.877 1774 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.55 % Allowed : 13.88 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.28 (0.23), residues: 1255 helix: 0.88 (0.22), residues: 510 sheet: 0.13 (0.32), residues: 252 loop : -0.40 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.010 0.001 HIS B 266 PHE 0.013 0.002 PHE A 222 TYR 0.012 0.002 TYR R 191 ARG 0.005 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 1.042 Fit side-chains REVERT: A 38 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6948 (mmt90) REVERT: A 60 MET cc_start: 0.4232 (mmp) cc_final: 0.3855 (mpp) REVERT: B 96 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7190 (mtm-85) REVERT: N 3 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: N 34 MET cc_start: 0.8798 (mmm) cc_final: 0.8255 (mmm) REVERT: R 91 SER cc_start: 0.0969 (OUTLIER) cc_final: 0.0671 (m) REVERT: R 141 LYS cc_start: 0.4812 (mmtt) cc_final: 0.4514 (tttt) REVERT: R 261 TRP cc_start: 0.6099 (m100) cc_final: 0.5757 (m100) REVERT: R 361 TRP cc_start: 0.6761 (t-100) cc_final: 0.6270 (t-100) REVERT: R 374 TYR cc_start: 0.5958 (m-80) cc_final: 0.5742 (m-80) outliers start: 27 outliers final: 6 residues processed: 166 average time/residue: 1.4310 time to fit residues: 252.6359 Evaluate side-chains 145 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 75 optimal weight: 0.0980 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 37 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 268 ASN N 5 GLN N 13 GLN P 14 ASN R 144 ASN R 179 GLN R 223 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10563 Z= 0.149 Angle : 0.503 6.667 14288 Z= 0.269 Chirality : 0.040 0.143 1577 Planarity : 0.004 0.042 1794 Dihedral : 9.342 139.341 1772 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.55 % Allowed : 14.83 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1255 helix: 1.70 (0.22), residues: 515 sheet: 0.21 (0.31), residues: 252 loop : -0.14 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS B 266 PHE 0.013 0.001 PHE A 212 TYR 0.011 0.001 TYR R 191 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.094 Fit side-chains REVERT: A 60 MET cc_start: 0.4195 (mmp) cc_final: 0.3833 (mpp) REVERT: B 96 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7131 (mtm-85) REVERT: G 21 MET cc_start: 0.6722 (tpp) cc_final: 0.6516 (mmp) REVERT: N 3 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: P 11 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.7132 (mtm-85) REVERT: R 141 LYS cc_start: 0.4968 (mmtt) cc_final: 0.4676 (tttt) REVERT: R 261 TRP cc_start: 0.6021 (m100) cc_final: 0.5713 (m100) REVERT: R 361 TRP cc_start: 0.6761 (t-100) cc_final: 0.6332 (t-100) REVERT: R 374 TYR cc_start: 0.5954 (m-80) cc_final: 0.5695 (m-80) outliers start: 27 outliers final: 7 residues processed: 154 average time/residue: 1.5452 time to fit residues: 252.5280 Evaluate side-chains 143 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 35 GLN B 13 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN P 10 GLN R 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10563 Z= 0.338 Angle : 0.731 7.834 14288 Z= 0.384 Chirality : 0.048 0.166 1577 Planarity : 0.006 0.041 1794 Dihedral : 11.244 139.593 1772 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.74 % Allowed : 14.83 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.63 (0.24), residues: 1255 helix: 1.22 (0.22), residues: 523 sheet: 0.24 (0.32), residues: 243 loop : -0.25 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 56 HIS 0.010 0.002 HIS B 266 PHE 0.019 0.003 PHE R 94 TYR 0.018 0.003 TYR R 146 ARG 0.007 0.001 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.141 Fit side-chains REVERT: A 60 MET cc_start: 0.4371 (mmp) cc_final: 0.3961 (mpp) REVERT: B 59 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: B 96 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7202 (mtm-85) REVERT: N 3 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: R 361 TRP cc_start: 0.6795 (t-100) cc_final: 0.6356 (t-100) outliers start: 29 outliers final: 14 residues processed: 141 average time/residue: 1.5727 time to fit residues: 235.0454 Evaluate side-chains 141 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN P 10 GLN R 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10563 Z= 0.173 Angle : 0.549 6.577 14288 Z= 0.292 Chirality : 0.041 0.143 1577 Planarity : 0.004 0.042 1794 Dihedral : 10.280 130.908 1772 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.36 % Allowed : 15.39 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.24), residues: 1255 helix: 1.67 (0.23), residues: 526 sheet: 0.34 (0.32), residues: 237 loop : -0.15 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.006 0.001 HIS B 266 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR R 92 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.083 Fit side-chains REVERT: A 60 MET cc_start: 0.4284 (mmp) cc_final: 0.3874 (mpp) REVERT: B 59 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: B 96 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7151 (mtm-85) REVERT: N 3 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: R 198 ILE cc_start: 0.6205 (mt) cc_final: 0.5977 (mm) REVERT: R 261 TRP cc_start: 0.6248 (m100) cc_final: 0.6020 (m100) REVERT: R 361 TRP cc_start: 0.6754 (t-100) cc_final: 0.6347 (t-100) outliers start: 25 outliers final: 12 residues processed: 144 average time/residue: 1.5517 time to fit residues: 237.1576 Evaluate side-chains 145 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.0070 chunk 113 optimal weight: 1.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 179 GLN R 226 HIS R 383 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10563 Z= 0.191 Angle : 0.568 6.354 14288 Z= 0.301 Chirality : 0.042 0.142 1577 Planarity : 0.004 0.042 1794 Dihedral : 10.248 128.711 1772 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.64 % Allowed : 15.58 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1255 helix: 1.76 (0.22), residues: 526 sheet: 0.28 (0.32), residues: 241 loop : -0.17 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.004 0.001 HIS B 266 PHE 0.012 0.002 PHE B 151 TYR 0.019 0.002 TYR R 338 ARG 0.007 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.129 Fit side-chains REVERT: A 60 MET cc_start: 0.4278 (mmp) cc_final: 0.3875 (mpp) REVERT: B 59 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: B 96 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7164 (mtm-85) REVERT: N 3 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: R 48 MET cc_start: 0.3635 (mmm) cc_final: 0.3282 (mmp) REVERT: R 198 ILE cc_start: 0.6214 (mt) cc_final: 0.5991 (mm) REVERT: R 361 TRP cc_start: 0.6681 (t-100) cc_final: 0.6316 (t-100) outliers start: 28 outliers final: 15 residues processed: 146 average time/residue: 1.5107 time to fit residues: 234.0122 Evaluate side-chains 147 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 117 optimal weight: 8.9990 chunk 73 optimal weight: 0.0670 chunk 71 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 88 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 179 GLN R 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10563 Z= 0.171 Angle : 0.552 9.455 14288 Z= 0.290 Chirality : 0.042 0.142 1577 Planarity : 0.004 0.043 1794 Dihedral : 9.987 128.041 1772 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.08 % Allowed : 15.68 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.24), residues: 1255 helix: 1.87 (0.22), residues: 526 sheet: 0.38 (0.33), residues: 237 loop : -0.17 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.006 0.001 HIS B 266 PHE 0.011 0.001 PHE B 151 TYR 0.020 0.002 TYR R 338 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.252 Fit side-chains REVERT: A 60 MET cc_start: 0.4268 (mmp) cc_final: 0.3861 (mpp) REVERT: B 59 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: B 96 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7159 (mtm-85) REVERT: N 3 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: R 198 ILE cc_start: 0.6203 (mt) cc_final: 0.5963 (mm) REVERT: R 361 TRP cc_start: 0.6654 (t-100) cc_final: 0.6322 (t-100) outliers start: 22 outliers final: 14 residues processed: 142 average time/residue: 1.5431 time to fit residues: 232.7481 Evaluate side-chains 147 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 88 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10563 Z= 0.198 Angle : 0.581 8.518 14288 Z= 0.305 Chirality : 0.042 0.143 1577 Planarity : 0.004 0.047 1794 Dihedral : 10.232 128.486 1772 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.64 % Allowed : 15.11 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1255 helix: 1.83 (0.22), residues: 524 sheet: 0.29 (0.32), residues: 239 loop : -0.23 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.007 0.001 HIS B 266 PHE 0.012 0.002 PHE B 151 TYR 0.022 0.002 TYR R 338 ARG 0.006 0.001 ARG P 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.212 Fit side-chains REVERT: A 60 MET cc_start: 0.4361 (mmp) cc_final: 0.3932 (mpp) REVERT: B 59 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8469 (m-80) REVERT: B 96 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7166 (mtm-85) REVERT: N 3 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: R 198 ILE cc_start: 0.6198 (mt) cc_final: 0.5987 (mm) REVERT: R 361 TRP cc_start: 0.6652 (t-100) cc_final: 0.6348 (t-100) outliers start: 28 outliers final: 18 residues processed: 146 average time/residue: 1.5230 time to fit residues: 236.2852 Evaluate side-chains 150 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 0.0970 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 390 GLN B 13 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10563 Z= 0.153 Angle : 0.533 8.764 14288 Z= 0.278 Chirality : 0.041 0.139 1577 Planarity : 0.004 0.045 1794 Dihedral : 9.842 128.754 1772 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.08 % Allowed : 15.68 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.24 (0.24), residues: 1255 helix: 2.01 (0.23), residues: 524 sheet: 0.39 (0.33), residues: 238 loop : -0.19 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.007 0.001 HIS B 266 PHE 0.011 0.001 PHE B 151 TYR 0.022 0.001 TYR R 338 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4270 (mmp) cc_final: 0.3856 (mpp) REVERT: B 59 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: B 96 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7110 (mtm-85) REVERT: N 3 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: R 198 ILE cc_start: 0.6203 (mt) cc_final: 0.5946 (mm) REVERT: R 361 TRP cc_start: 0.6584 (t-100) cc_final: 0.6319 (t-100) outliers start: 22 outliers final: 13 residues processed: 144 average time/residue: 1.5708 time to fit residues: 240.3831 Evaluate side-chains 145 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 80 optimal weight: 0.1980 chunk 121 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 0.0370 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10563 Z= 0.156 Angle : 0.528 8.850 14288 Z= 0.276 Chirality : 0.041 0.139 1577 Planarity : 0.004 0.046 1794 Dihedral : 9.635 126.697 1772 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.89 % Allowed : 15.86 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.33 (0.24), residues: 1255 helix: 2.11 (0.22), residues: 525 sheet: 0.39 (0.33), residues: 238 loop : -0.16 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.011 0.001 PHE B 151 TYR 0.023 0.001 TYR R 338 ARG 0.011 0.000 ARG P 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.194 Fit side-chains REVERT: A 60 MET cc_start: 0.4241 (mmp) cc_final: 0.3898 (mpp) REVERT: B 59 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: B 96 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7131 (mtm-85) REVERT: N 3 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: R 361 TRP cc_start: 0.6485 (t-100) cc_final: 0.6231 (t-100) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 1.4923 time to fit residues: 217.0521 Evaluate side-chains 140 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 271 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 99 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 390 GLN B 13 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.219460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.188990 restraints weight = 8055.432| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 0.75 r_work: 0.3919 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10563 Z= 0.190 Angle : 0.578 8.728 14288 Z= 0.301 Chirality : 0.042 0.141 1577 Planarity : 0.004 0.051 1794 Dihedral : 9.998 126.778 1772 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.89 % Allowed : 15.96 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.21 (0.24), residues: 1255 helix: 1.94 (0.22), residues: 526 sheet: 0.43 (0.33), residues: 236 loop : -0.19 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.012 0.002 PHE B 151 TYR 0.024 0.002 TYR R 338 ARG 0.007 0.001 ARG P 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4575.75 seconds wall clock time: 81 minutes 20.97 seconds (4880.97 seconds total)