Starting phenix.real_space_refine on Fri Mar 15 18:47:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gd9_29943/03_2024/8gd9_29943_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gd9_29943/03_2024/8gd9_29943.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gd9_29943/03_2024/8gd9_29943_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gd9_29943/03_2024/8gd9_29943_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gd9_29943/03_2024/8gd9_29943_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gd9_29943/03_2024/8gd9_29943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gd9_29943/03_2024/8gd9_29943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gd9_29943/03_2024/8gd9_29943_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gd9_29943/03_2024/8gd9_29943_neut_updated.pdb" } resolution = 3.2 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5199 atoms to isotropic. 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 45 5.16 5 C 4670 2.51 5 N 1281 2.21 5 O 1313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 212": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R GLU 267": "OE1" <-> "OE2" Residue "R ARG 333": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7309 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1603 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 126 Chain: "B" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2430 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 3, 'HIS:plan': 1, 'ASN%COO:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 138 Chain: "G" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 362 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "N" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 905 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1979 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Z2C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.95, per 1000 atoms: 0.54 Number of scatterers: 7309 At special positions: 0 Unit cell: (98.6, 115.6, 96.9, 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 45 16.00 O 1313 8.00 N 1281 7.00 C 4670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.05 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.05 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: 2.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 10 sheets defined 36.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.833A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 239 removed outlier: 3.906A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 236 through 239' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.874A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.894A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 removed outlier: 3.637A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.807A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 22 removed outlier: 3.528A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 23 through 43 Processing helix chain 'R' and resid 49 through 51 No H-bonds generated for 'chain 'R' and resid 49 through 51' Processing helix chain 'R' and resid 54 through 82 removed outlier: 3.869A pdb=" N LEU R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL R 72 " --> pdb=" O GLY R 68 " (cutoff:3.500A) Proline residue: R 74 - end of helix removed outlier: 3.925A pdb=" N LYS R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 122 removed outlier: 3.604A pdb=" N PHE R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 130 Processing helix chain 'R' and resid 135 through 152 removed outlier: 3.586A pdb=" N ALA R 142 " --> pdb=" O LEU R 138 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE R 150 " --> pdb=" O SER R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 156 No H-bonds generated for 'chain 'R' and resid 154 through 156' Processing helix chain 'R' and resid 179 through 220 removed outlier: 3.534A pdb=" N ALA R 189 " --> pdb=" O SER R 185 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS R 207 " --> pdb=" O ASN R 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG R 212 " --> pdb=" O GLY R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 297 Proline residue: R 287 - end of helix removed outlier: 3.779A pdb=" N LEU R 297 " --> pdb=" O PHE R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 329 removed outlier: 3.909A pdb=" N ILE R 315 " --> pdb=" O ASP R 311 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL R 320 " --> pdb=" O ARG R 316 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) Proline residue: R 322 - end of helix Proline residue: R 326 - end of helix Processing helix chain 'R' and resid 334 through 340 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 4.190A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.688A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.788A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.954A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.873A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.629A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.699A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 4 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.009A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 1002 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: 2.18 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1185 1.31 - 1.45: 2128 1.45 - 1.59: 4078 1.59 - 1.72: 2 1.72 - 1.86: 60 Bond restraints: 7453 Sorted by residual: bond pdb=" C8 Z2C R 501 " pdb=" C9 Z2C R 501 " ideal model delta sigma weight residual 1.587 1.310 0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C5 Z2C R 501 " pdb=" C9 Z2C R 501 " ideal model delta sigma weight residual 1.386 1.597 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C7 Z2C R 501 " pdb=" C8 Z2C R 501 " ideal model delta sigma weight residual 1.399 1.568 -0.169 2.00e-02 2.50e+03 7.10e+01 bond pdb=" C5 Z2C R 501 " pdb=" C6 Z2C R 501 " ideal model delta sigma weight residual 1.690 1.582 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" CA THR B 87 " pdb=" C THR B 87 " ideal model delta sigma weight residual 1.527 1.459 0.068 1.27e-02 6.20e+03 2.85e+01 ... (remaining 7448 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.89: 117 105.89 - 112.97: 3949 112.97 - 120.06: 2633 120.06 - 127.14: 3402 127.14 - 134.22: 75 Bond angle restraints: 10176 Sorted by residual: angle pdb=" N LYS G 14 " pdb=" CA LYS G 14 " pdb=" C LYS G 14 " ideal model delta sigma weight residual 111.36 119.25 -7.89 1.09e+00 8.42e-01 5.24e+01 angle pdb=" N LYS R 334 " pdb=" CA LYS R 334 " pdb=" C LYS R 334 " ideal model delta sigma weight residual 111.71 120.03 -8.32 1.15e+00 7.56e-01 5.23e+01 angle pdb=" N ALA B 309 " pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 113.17 122.24 -9.07 1.26e+00 6.30e-01 5.19e+01 angle pdb=" N THR R 335 " pdb=" CA THR R 335 " pdb=" C THR R 335 " ideal model delta sigma weight residual 111.07 118.62 -7.55 1.07e+00 8.73e-01 4.98e+01 angle pdb=" N TYR A 358 " pdb=" CA TYR A 358 " pdb=" C TYR A 358 " ideal model delta sigma weight residual 111.28 120.41 -9.13 1.35e+00 5.49e-01 4.58e+01 ... (remaining 10171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4006 17.35 - 34.71: 268 34.71 - 52.06: 51 52.06 - 69.41: 16 69.41 - 86.77: 7 Dihedral angle restraints: 4348 sinusoidal: 1398 harmonic: 2950 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 153.74 26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ILE R 330 " pdb=" C ILE R 330 " pdb=" N LEU R 331 " pdb=" CA LEU R 331 " ideal model delta harmonic sigma weight residual 180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS R 129 " pdb=" C HIS R 129 " pdb=" N TYR R 130 " pdb=" CA TYR R 130 " ideal model delta harmonic sigma weight residual -180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 4345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1049 0.090 - 0.179: 146 0.179 - 0.269: 11 0.269 - 0.358: 5 0.358 - 0.448: 2 Chirality restraints: 1213 Sorted by residual: chirality pdb=" CA ASN R 35 " pdb=" N ASN R 35 " pdb=" C ASN R 35 " pdb=" CB ASN R 35 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA LYS G 14 " pdb=" N LYS G 14 " pdb=" C LYS G 14 " pdb=" CB LYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 1210 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 151 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C CYS R 151 " -0.059 2.00e-02 2.50e+03 pdb=" O CYS R 151 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA R 152 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 185 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C SER R 185 " 0.055 2.00e-02 2.50e+03 pdb=" O SER R 185 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR R 186 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 85 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.79e+00 pdb=" C TYR B 85 " 0.051 2.00e-02 2.50e+03 pdb=" O TYR B 85 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 86 " -0.017 2.00e-02 2.50e+03 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1058 2.76 - 3.29: 6709 3.29 - 3.83: 11624 3.83 - 4.36: 13639 4.36 - 4.90: 24319 Nonbonded interactions: 57349 Sorted by model distance: nonbonded pdb=" O ASN R 321 " pdb=" OD2 ASP R 325 " model vdw 2.224 3.040 nonbonded pdb=" O LEU A 346 " pdb=" OG1 THR A 350 " model vdw 2.251 2.440 nonbonded pdb=" O GLY B 224 " pdb=" NH1 ARG B 251 " model vdw 2.336 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.348 2.440 nonbonded pdb=" O PHE N 29 " pdb=" NH2 ARG N 72 " model vdw 2.361 2.520 ... (remaining 57344 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: 0.010 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 3.670 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.430 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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 : 0.009 0.277 7453 Z= 0.575 Angle : 1.029 10.965 10176 Z= 0.632 Chirality : 0.064 0.448 1213 Planarity : 0.006 0.063 1296 Dihedral : 13.467 86.765 2429 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.30 % Allowed : 0.91 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.25), residues: 995 helix: 0.19 (0.26), residues: 371 sheet: -0.38 (0.34), residues: 229 loop : -1.73 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 339 HIS 0.007 0.002 HIS B 225 PHE 0.024 0.003 PHE A 246 TYR 0.019 0.002 TYR R 298 ARG 0.010 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8081 (tt) cc_final: 0.7877 (tp) REVERT: B 137 ARG cc_start: 0.7335 (tpp-160) cc_final: 0.7092 (tpp80) REVERT: B 239 ASN cc_start: 0.8148 (m110) cc_final: 0.7752 (m-40) REVERT: R 169 TRP cc_start: 0.8035 (p-90) cc_final: 0.7691 (p-90) REVERT: R 270 MET cc_start: 0.7692 (tpt) cc_final: 0.7390 (tpt) outliers start: 2 outliers final: 2 residues processed: 167 average time/residue: 0.2098 time to fit residues: 45.6385 Evaluate side-chains 158 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 88 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN R 129 HIS R 216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7453 Z= 0.236 Angle : 0.554 6.123 10176 Z= 0.297 Chirality : 0.043 0.144 1213 Planarity : 0.004 0.053 1296 Dihedral : 7.132 76.509 1107 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.83 % Allowed : 8.68 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 995 helix: 1.38 (0.27), residues: 367 sheet: -0.12 (0.35), residues: 216 loop : -1.51 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.002 PHE N 108 TYR 0.014 0.002 TYR A 339 ARG 0.003 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8057 (m110) cc_final: 0.7733 (m-40) REVERT: B 245 SER cc_start: 0.7892 (p) cc_final: 0.7612 (t) REVERT: B 291 ASP cc_start: 0.7165 (p0) cc_final: 0.6957 (p0) REVERT: B 329 THR cc_start: 0.8030 (p) cc_final: 0.7723 (m) REVERT: G 19 LEU cc_start: 0.7882 (mt) cc_final: 0.7478 (mp) REVERT: N 21 SER cc_start: 0.8149 (m) cc_final: 0.7941 (t) REVERT: R 107 LEU cc_start: 0.8149 (tp) cc_final: 0.7874 (tp) outliers start: 12 outliers final: 10 residues processed: 171 average time/residue: 0.2089 time to fit residues: 46.7136 Evaluate side-chains 165 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 90 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 HIS R 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7453 Z= 0.147 Angle : 0.482 5.234 10176 Z= 0.257 Chirality : 0.041 0.146 1213 Planarity : 0.003 0.048 1296 Dihedral : 6.518 76.429 1104 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.52 % Allowed : 14.16 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 995 helix: 2.03 (0.28), residues: 370 sheet: 0.03 (0.35), residues: 220 loop : -1.19 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.019 0.001 PHE R 54 TYR 0.012 0.001 TYR A 339 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 0.828 Fit side-chains REVERT: A 246 PHE cc_start: 0.7984 (t80) cc_final: 0.7422 (t80) REVERT: B 239 ASN cc_start: 0.8071 (m110) cc_final: 0.7714 (m-40) REVERT: B 289 TYR cc_start: 0.8162 (m-80) cc_final: 0.7651 (m-80) REVERT: B 291 ASP cc_start: 0.7093 (p0) cc_final: 0.6869 (p0) REVERT: B 329 THR cc_start: 0.8011 (p) cc_final: 0.7727 (m) REVERT: N 21 SER cc_start: 0.8113 (m) cc_final: 0.7905 (t) REVERT: R 40 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.8043 (t) REVERT: R 107 LEU cc_start: 0.8141 (tp) cc_final: 0.7852 (tp) outliers start: 10 outliers final: 6 residues processed: 157 average time/residue: 0.2065 time to fit residues: 42.6600 Evaluate side-chains 154 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 319 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 95 optimal weight: 0.0370 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7453 Z= 0.184 Angle : 0.490 5.469 10176 Z= 0.261 Chirality : 0.041 0.145 1213 Planarity : 0.003 0.044 1296 Dihedral : 6.405 75.882 1104 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.44 % Allowed : 16.89 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 995 helix: 2.14 (0.28), residues: 376 sheet: 0.11 (0.35), residues: 221 loop : -1.06 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.002 PHE R 54 TYR 0.012 0.001 TYR A 339 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.022 Fit side-chains REVERT: B 239 ASN cc_start: 0.8068 (m110) cc_final: 0.7726 (m-40) REVERT: B 289 TYR cc_start: 0.8145 (m-80) cc_final: 0.7686 (m-80) REVERT: B 291 ASP cc_start: 0.7136 (p0) cc_final: 0.6924 (p0) REVERT: B 329 THR cc_start: 0.7990 (p) cc_final: 0.7720 (m) REVERT: R 40 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8050 (t) REVERT: R 107 LEU cc_start: 0.8131 (tp) cc_final: 0.7877 (tp) outliers start: 16 outliers final: 10 residues processed: 151 average time/residue: 0.2129 time to fit residues: 41.8621 Evaluate side-chains 155 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7453 Z= 0.353 Angle : 0.581 8.116 10176 Z= 0.310 Chirality : 0.045 0.165 1213 Planarity : 0.004 0.044 1296 Dihedral : 6.789 78.553 1104 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.35 % Allowed : 16.29 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 995 helix: 1.89 (0.27), residues: 378 sheet: 0.04 (0.35), residues: 229 loop : -0.95 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.007 0.002 HIS A 357 PHE 0.021 0.002 PHE N 108 TYR 0.020 0.002 TYR N 95 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8039 (m110) cc_final: 0.7747 (m-40) REVERT: B 291 ASP cc_start: 0.7285 (p0) cc_final: 0.6893 (p0) REVERT: B 329 THR cc_start: 0.7892 (p) cc_final: 0.7687 (m) outliers start: 22 outliers final: 17 residues processed: 161 average time/residue: 0.2115 time to fit residues: 44.6396 Evaluate side-chains 169 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 0.0670 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7453 Z= 0.139 Angle : 0.465 5.118 10176 Z= 0.250 Chirality : 0.041 0.147 1213 Planarity : 0.003 0.043 1296 Dihedral : 6.336 79.170 1104 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.59 % Allowed : 17.35 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 995 helix: 2.18 (0.27), residues: 381 sheet: 0.31 (0.37), residues: 211 loop : -0.93 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.019 0.001 PHE R 54 TYR 0.010 0.001 TYR A 339 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 0.938 Fit side-chains REVERT: B 239 ASN cc_start: 0.8025 (m110) cc_final: 0.7773 (m-40) REVERT: B 289 TYR cc_start: 0.8223 (m-80) cc_final: 0.7688 (m-80) REVERT: B 291 ASP cc_start: 0.7163 (p0) cc_final: 0.6962 (p0) REVERT: N 21 SER cc_start: 0.8092 (m) cc_final: 0.7776 (p) REVERT: R 40 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.8060 (t) REVERT: R 76 THR cc_start: 0.8626 (m) cc_final: 0.8328 (p) REVERT: R 107 LEU cc_start: 0.8077 (tp) cc_final: 0.7820 (tp) outliers start: 17 outliers final: 15 residues processed: 163 average time/residue: 0.2111 time to fit residues: 44.9796 Evaluate side-chains 172 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 69 optimal weight: 0.0770 chunk 80 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 0.0570 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7453 Z= 0.214 Angle : 0.505 6.308 10176 Z= 0.267 Chirality : 0.042 0.146 1213 Planarity : 0.003 0.041 1296 Dihedral : 6.389 80.504 1104 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.59 % Allowed : 17.81 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.28), residues: 995 helix: 2.15 (0.27), residues: 381 sheet: 0.33 (0.36), residues: 220 loop : -0.84 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.002 PHE R 54 TYR 0.014 0.001 TYR N 95 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8014 (m110) cc_final: 0.7814 (m-40) REVERT: B 258 ASP cc_start: 0.7445 (t0) cc_final: 0.7037 (t0) REVERT: B 289 TYR cc_start: 0.8227 (m-80) cc_final: 0.7709 (m-80) REVERT: B 291 ASP cc_start: 0.7245 (p0) cc_final: 0.7036 (p0) REVERT: N 21 SER cc_start: 0.8115 (m) cc_final: 0.7771 (p) REVERT: R 40 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8063 (t) REVERT: R 76 THR cc_start: 0.8612 (m) cc_final: 0.8324 (p) outliers start: 17 outliers final: 15 residues processed: 160 average time/residue: 0.2272 time to fit residues: 47.5461 Evaluate side-chains 169 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7453 Z= 0.252 Angle : 0.529 6.638 10176 Z= 0.281 Chirality : 0.043 0.143 1213 Planarity : 0.004 0.040 1296 Dihedral : 6.451 82.259 1104 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.04 % Allowed : 17.50 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.28), residues: 995 helix: 2.07 (0.27), residues: 381 sheet: 0.22 (0.36), residues: 225 loop : -0.78 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.002 PHE R 54 TYR 0.016 0.002 TYR N 95 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: B 289 TYR cc_start: 0.8221 (m-80) cc_final: 0.7725 (m-80) REVERT: B 291 ASP cc_start: 0.7275 (p0) cc_final: 0.7073 (p0) REVERT: N 21 SER cc_start: 0.8085 (m) cc_final: 0.7751 (p) REVERT: R 40 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8085 (t) REVERT: R 76 THR cc_start: 0.8583 (m) cc_final: 0.8352 (p) REVERT: R 107 LEU cc_start: 0.8026 (tp) cc_final: 0.7762 (tp) outliers start: 20 outliers final: 16 residues processed: 161 average time/residue: 0.2084 time to fit residues: 44.0976 Evaluate side-chains 169 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.0000 chunk 27 optimal weight: 0.1980 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN R 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7453 Z= 0.164 Angle : 0.483 7.173 10176 Z= 0.256 Chirality : 0.041 0.146 1213 Planarity : 0.003 0.041 1296 Dihedral : 6.126 80.652 1104 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.44 % Allowed : 18.72 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.28), residues: 995 helix: 2.24 (0.27), residues: 383 sheet: 0.33 (0.36), residues: 216 loop : -0.80 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE R 54 TYR 0.011 0.001 TYR N 95 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 0.815 Fit side-chains REVERT: B 150 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7911 (mmt180) REVERT: B 258 ASP cc_start: 0.7575 (t0) cc_final: 0.7364 (t0) REVERT: B 277 SER cc_start: 0.8476 (p) cc_final: 0.8210 (t) REVERT: B 289 TYR cc_start: 0.8191 (m-80) cc_final: 0.7715 (m-80) REVERT: B 291 ASP cc_start: 0.7244 (p0) cc_final: 0.7041 (p0) REVERT: N 21 SER cc_start: 0.8093 (m) cc_final: 0.7782 (p) REVERT: R 40 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8090 (t) REVERT: R 76 THR cc_start: 0.8555 (m) cc_final: 0.8332 (p) REVERT: R 107 LEU cc_start: 0.8023 (tp) cc_final: 0.7777 (tp) outliers start: 16 outliers final: 14 residues processed: 160 average time/residue: 0.2134 time to fit residues: 44.3747 Evaluate side-chains 169 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 78 optimal weight: 0.0050 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7453 Z= 0.190 Angle : 0.494 6.714 10176 Z= 0.262 Chirality : 0.041 0.145 1213 Planarity : 0.003 0.041 1296 Dihedral : 6.115 80.537 1104 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.59 % Allowed : 18.42 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.28), residues: 995 helix: 2.27 (0.27), residues: 383 sheet: 0.33 (0.36), residues: 216 loop : -0.77 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.002 PHE R 54 TYR 0.013 0.001 TYR N 95 ARG 0.004 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.157 Fit side-chains REVERT: B 150 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7911 (mmt180) REVERT: B 258 ASP cc_start: 0.7590 (t0) cc_final: 0.7358 (t0) REVERT: B 289 TYR cc_start: 0.8193 (m-80) cc_final: 0.7722 (m-80) REVERT: N 21 SER cc_start: 0.8105 (m) cc_final: 0.7789 (p) REVERT: R 40 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8097 (t) REVERT: R 76 THR cc_start: 0.8592 (m) cc_final: 0.8337 (p) outliers start: 17 outliers final: 14 residues processed: 162 average time/residue: 0.2104 time to fit residues: 44.6105 Evaluate side-chains 170 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 78 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.128968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108463 restraints weight = 9987.418| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.55 r_work: 0.3169 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7453 Z= 0.209 Angle : 0.502 6.751 10176 Z= 0.267 Chirality : 0.042 0.144 1213 Planarity : 0.003 0.041 1296 Dihedral : 6.126 80.239 1104 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.59 % Allowed : 18.72 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.28), residues: 995 helix: 2.26 (0.27), residues: 383 sheet: 0.33 (0.36), residues: 222 loop : -0.76 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.002 PHE R 54 TYR 0.014 0.001 TYR N 95 ARG 0.005 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.91 seconds wall clock time: 37 minutes 40.28 seconds (2260.28 seconds total)