Starting phenix.real_space_refine on Tue Feb 13 23:35:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfm_30344/02_2024/7cfm_30344_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfm_30344/02_2024/7cfm_30344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfm_30344/02_2024/7cfm_30344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfm_30344/02_2024/7cfm_30344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfm_30344/02_2024/7cfm_30344_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfm_30344/02_2024/7cfm_30344_updated.pdb" } resolution = 3.0 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5140 2.51 5 N 1419 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 187": "NH1" <-> "NH2" Residue "R ARG 201": "NH1" <-> "NH2" Residue "R ARG 204": "NH1" <-> "NH2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 221": "NH1" <-> "NH2" Residue "R ARG 224": "NH1" <-> "NH2" Residue "R ARG 254": "NH1" <-> "NH2" Residue "R ARG 286": "NH1" <-> "NH2" Residue "R ARG 292": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8081 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1897 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 229, 1886 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "C" Number of residues, atoms: 229, 1886 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1910 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2177 Unusual residues: {'CLR': 3, 'FWX': 1} Classifications: {'peptide': 273, 'undetermined': 4, 'water': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 251, None: 5} Not linked: pdbres="ARG R 292 " pdbres="FWX R 401 " Not linked: pdbres="FWX R 401 " pdbres="CLR R 402 " Not linked: pdbres="CLR R 402 " pdbres="CLR R 403 " Not linked: pdbres="CLR R 403 " pdbres="CLR R 404 " Not linked: pdbres="CLR R 404 " pdbres="HOH R 501 " Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 380 " occ=0.50 ... (20 atoms not shown) pdb=" NH2CARG A 380 " occ=0.62 Time building chain proxies: 5.81, per 1000 atoms: 0.72 Number of scatterers: 8081 At special positions: 0 Unit cell: (79.092, 113.568, 122.694, 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 46 16.00 O 1476 8.00 N 1419 7.00 C 5140 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=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 155 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.9 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 11 sheets defined 37.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.889A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.922A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.889A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.667A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.029A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 removed outlier: 4.097A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 47 removed outlier: 5.252A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'R' and resid 22 through 41 Processing helix chain 'R' and resid 45 through 47 No H-bonds generated for 'chain 'R' and resid 45 through 47' Processing helix chain 'R' and resid 49 through 67 Processing helix chain 'R' and resid 82 through 115 removed outlier: 3.921A pdb=" N LEU R 87 " --> pdb=" O TRP R 83 " (cutoff:3.500A) Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 124 through 144 removed outlier: 3.872A pdb=" N GLY R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Proline residue: R 135 - end of helix Proline residue: R 142 - end of helix Processing helix chain 'R' and resid 157 through 160 No H-bonds generated for 'chain 'R' and resid 157 through 160' Processing helix chain 'R' and resid 163 through 172 Processing helix chain 'R' and resid 174 through 206 removed outlier: 3.522A pdb=" N VAL R 178 " --> pdb=" O LEU R 174 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 251 removed outlier: 3.730A pdb=" N ALA R 217 " --> pdb=" O ALA R 213 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY R 238 " --> pdb=" O GLY R 234 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 263 through 283 Proline residue: R 277 - end of helix removed outlier: 3.548A pdb=" N GLY R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 4.145A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 217 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.004A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.814A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 148 through 151 removed outlier: 4.103A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.975A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.460A 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: 6.642A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.700A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.813A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 165 through 170 removed outlier: 6.377A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.509A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.554A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1036 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: 2.53 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2594 1.34 - 1.46: 1957 1.46 - 1.59: 3645 1.59 - 1.71: 0 1.71 - 1.84: 63 Bond restraints: 8259 Sorted by residual: bond pdb=" C04 FWX R 401 " pdb=" N03 FWX R 401 " ideal model delta sigma weight residual 1.343 1.423 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C12 FWX R 401 " pdb=" N09 FWX R 401 " ideal model delta sigma weight residual 1.351 1.425 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C04 FWX R 401 " pdb=" N26 FWX R 401 " ideal model delta sigma weight residual 1.329 1.402 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C LYS N 87 " pdb=" N PRO N 88 " ideal model delta sigma weight residual 1.337 1.365 -0.028 9.80e-03 1.04e+04 8.35e+00 bond pdb=" C06 FWX R 401 " pdb=" N05 FWX R 401 " ideal model delta sigma weight residual 1.319 1.368 -0.049 2.00e-02 2.50e+03 5.94e+00 ... (remaining 8254 not shown) Histogram of bond angle deviations from ideal: 94.67 - 102.55: 22 102.55 - 110.44: 2121 110.44 - 118.32: 4235 118.32 - 126.20: 4699 126.20 - 134.09: 155 Bond angle restraints: 11232 Sorted by residual: angle pdb=" C LYS B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 122.46 128.54 -6.08 1.41e+00 5.03e-01 1.86e+01 angle pdb=" N LEU R 45 " pdb=" CA LEU R 45 " pdb=" C LEU R 45 " ideal model delta sigma weight residual 111.36 115.87 -4.51 1.09e+00 8.42e-01 1.71e+01 angle pdb=" N GLY A 47 " pdb=" CA GLY A 47 " pdb=" C GLY A 47 " ideal model delta sigma weight residual 113.18 104.68 8.50 2.37e+00 1.78e-01 1.29e+01 angle pdb=" C PRO R 259 " pdb=" N GLY R 260 " pdb=" CA GLY R 260 " ideal model delta sigma weight residual 121.41 128.28 -6.87 1.96e+00 2.60e-01 1.23e+01 angle pdb=" CB MET B 262 " pdb=" CG MET B 262 " pdb=" SD MET B 262 " ideal model delta sigma weight residual 112.70 123.11 -10.41 3.00e+00 1.11e-01 1.20e+01 ... (remaining 11227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4798 17.38 - 34.77: 210 34.77 - 52.15: 39 52.15 - 69.53: 9 69.53 - 86.92: 11 Dihedral angle restraints: 5067 sinusoidal: 2096 harmonic: 2971 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -7.94 -78.06 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CA LYS B 301 " pdb=" C LYS B 301 " pdb=" N ALA B 302 " pdb=" CA ALA B 302 " ideal model delta harmonic sigma weight residual 180.00 152.55 27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual -86.00 -127.69 41.69 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 5064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1102 0.092 - 0.185: 148 0.185 - 0.277: 13 0.277 - 0.369: 1 0.369 - 0.462: 1 Chirality restraints: 1265 Sorted by residual: chirality pdb=" C20 CLR R 402 " pdb=" C17 CLR R 402 " pdb=" C21 CLR R 402 " pdb=" C22 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.59 2.13 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" C17 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C16 CLR R 402 " pdb=" C20 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB THR N 28 " pdb=" CA THR N 28 " pdb=" OG1 THR N 28 " pdb=" CG2 THR N 28 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1262 not shown) Planarity restraints: 1428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.73e+00 pdb=" N PRO B 236 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " -0.021 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" CG TRP A 281 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO A 332 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.029 5.00e-02 4.00e+02 ... (remaining 1425 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 37 2.57 - 3.15: 5986 3.15 - 3.74: 12230 3.74 - 4.32: 16695 4.32 - 4.90: 28533 Nonbonded interactions: 63481 Sorted by model distance: nonbonded pdb=" O ASN A 54 " pdb=" CD LYS A 58 " model vdw 1.988 3.440 nonbonded pdb=" OH TYR R 167 " pdb=" OE2 GLU R 252 " model vdw 2.290 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.293 2.440 nonbonded pdb=" O ASP N 90 " pdb=" OH TYR N 94 " model vdw 2.308 2.440 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.322 2.440 ... (remaining 63476 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.900 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.990 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 : 0.006 0.080 8259 Z= 0.389 Angle : 0.989 10.451 11232 Z= 0.517 Chirality : 0.062 0.462 1265 Planarity : 0.007 0.060 1428 Dihedral : 11.281 86.917 3142 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.24 % Allowed : 4.17 % Favored : 95.60 % 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: -2.23 (0.22), residues: 1016 helix: -1.26 (0.20), residues: 393 sheet: -0.89 (0.32), residues: 228 loop : -1.89 (0.26), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 281 HIS 0.011 0.003 HIS B 54 PHE 0.020 0.003 PHE A 212 TYR 0.022 0.003 TYR A 339 ARG 0.013 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7492 (ptt) cc_final: 0.7046 (pp-130) REVERT: B 228 ASP cc_start: 0.7736 (p0) cc_final: 0.7300 (p0) REVERT: B 270 ILE cc_start: 0.8285 (pp) cc_final: 0.7912 (pp) REVERT: G 21 MET cc_start: 0.7609 (tpt) cc_final: 0.7066 (mmm) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 1.1983 time to fit residues: 238.3457 Evaluate side-chains 105 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 294 GLN B 110 ASN B 230 ASN N 77 ASN R 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8259 Z= 0.171 Angle : 0.595 8.055 11232 Z= 0.294 Chirality : 0.043 0.191 1265 Planarity : 0.005 0.039 1428 Dihedral : 7.541 86.140 1332 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.21 % Allowed : 11.90 % Favored : 84.88 % 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: -0.49 (0.24), residues: 1016 helix: 0.83 (0.24), residues: 396 sheet: -0.44 (0.33), residues: 223 loop : -1.38 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE N 108 TYR 0.017 0.001 TYR A 339 ARG 0.007 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 14 LEU cc_start: 0.8019 (mt) cc_final: 0.7573 (mp) REVERT: B 217 MET cc_start: 0.7516 (ptt) cc_final: 0.7272 (pmt) REVERT: B 228 ASP cc_start: 0.7721 (p0) cc_final: 0.7499 (p0) REVERT: B 270 ILE cc_start: 0.8261 (pp) cc_final: 0.7888 (pp) REVERT: B 280 LYS cc_start: 0.8717 (tttm) cc_final: 0.8451 (ttpt) REVERT: G 21 MET cc_start: 0.7609 (tpt) cc_final: 0.7019 (mmm) REVERT: N 77 ASN cc_start: 0.7800 (m-40) cc_final: 0.7310 (t0) REVERT: R 141 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7771 (mt) outliers start: 27 outliers final: 8 residues processed: 150 average time/residue: 1.1255 time to fit residues: 180.2879 Evaluate side-chains 120 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 149 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 75 optimal weight: 0.0770 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 0.0670 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 292 ASN B 35 ASN N 39 GLN R 119 GLN R 154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8259 Z= 0.129 Angle : 0.532 8.823 11232 Z= 0.258 Chirality : 0.042 0.176 1265 Planarity : 0.004 0.066 1428 Dihedral : 7.072 85.194 1332 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.45 % Allowed : 14.17 % Favored : 82.38 % 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: 0.35 (0.26), residues: 1016 helix: 1.76 (0.26), residues: 398 sheet: -0.05 (0.35), residues: 211 loop : -1.16 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.017 0.001 TYR A 339 ARG 0.008 0.000 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8360 (mttp) REVERT: A 283 ARG cc_start: 0.7757 (mpt-90) cc_final: 0.7018 (mmm-85) REVERT: B 98 SER cc_start: 0.8655 (m) cc_final: 0.8439 (p) REVERT: B 212 ASP cc_start: 0.7885 (t70) cc_final: 0.7489 (t70) REVERT: B 217 MET cc_start: 0.7519 (ptt) cc_final: 0.7248 (pmt) REVERT: B 228 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7358 (p0) REVERT: B 270 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7995 (pp) REVERT: B 280 LYS cc_start: 0.8690 (tttm) cc_final: 0.8439 (ttpt) REVERT: G 21 MET cc_start: 0.7652 (tpt) cc_final: 0.7043 (mmm) REVERT: R 79 ARG cc_start: 0.8101 (tpp80) cc_final: 0.7884 (tpp80) REVERT: R 119 GLN cc_start: 0.7871 (tt0) cc_final: 0.7585 (tt0) outliers start: 29 outliers final: 8 residues processed: 136 average time/residue: 1.0204 time to fit residues: 148.9787 Evaluate side-chains 123 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 149 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 39 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8259 Z= 0.237 Angle : 0.571 8.510 11232 Z= 0.280 Chirality : 0.044 0.204 1265 Planarity : 0.004 0.043 1428 Dihedral : 6.920 88.270 1332 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.05 % Allowed : 13.81 % Favored : 82.14 % 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: 0.57 (0.26), residues: 1016 helix: 2.06 (0.26), residues: 393 sheet: 0.03 (0.35), residues: 213 loop : -1.11 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.023 0.002 PHE N 108 TYR 0.021 0.001 TYR A 339 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8372 (mttp) REVERT: A 392 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7496 (mm-30) REVERT: B 212 ASP cc_start: 0.7925 (t70) cc_final: 0.7522 (t70) REVERT: B 217 MET cc_start: 0.7560 (ptt) cc_final: 0.7175 (pmt) REVERT: B 228 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7424 (p0) REVERT: B 270 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7958 (pp) REVERT: B 280 LYS cc_start: 0.8648 (tttm) cc_final: 0.8434 (ttpt) REVERT: G 21 MET cc_start: 0.7677 (tpt) cc_final: 0.7098 (mmm) REVERT: N 5 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7479 (mm-40) REVERT: N 60 TYR cc_start: 0.8910 (m-80) cc_final: 0.8661 (m-80) REVERT: N 77 ASN cc_start: 0.7800 (m-40) cc_final: 0.7335 (t0) outliers start: 34 outliers final: 15 residues processed: 139 average time/residue: 1.0302 time to fit residues: 153.4216 Evaluate side-chains 131 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN R 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8259 Z= 0.221 Angle : 0.552 8.859 11232 Z= 0.272 Chirality : 0.043 0.207 1265 Planarity : 0.004 0.044 1428 Dihedral : 6.892 89.410 1332 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.21 % Allowed : 16.07 % Favored : 80.71 % 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: 0.73 (0.26), residues: 1016 helix: 2.21 (0.26), residues: 393 sheet: 0.02 (0.36), residues: 207 loop : -0.96 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.002 PHE N 108 TYR 0.020 0.001 TYR A 339 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8413 (mttp) REVERT: A 392 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7493 (mm-30) REVERT: B 212 ASP cc_start: 0.7876 (t70) cc_final: 0.7472 (t70) REVERT: B 228 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7449 (p0) REVERT: B 270 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7944 (pp) REVERT: B 280 LYS cc_start: 0.8665 (tttm) cc_final: 0.8449 (ttpt) REVERT: G 21 MET cc_start: 0.7441 (tpt) cc_final: 0.6914 (mmm) REVERT: N 5 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7434 (mm-40) REVERT: R 97 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7478 (mt) outliers start: 27 outliers final: 14 residues processed: 128 average time/residue: 1.0468 time to fit residues: 143.7856 Evaluate side-chains 124 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8259 Z= 0.199 Angle : 0.545 10.842 11232 Z= 0.264 Chirality : 0.043 0.194 1265 Planarity : 0.004 0.044 1428 Dihedral : 6.816 88.406 1332 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.10 % Allowed : 17.14 % Favored : 79.76 % 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: 0.85 (0.26), residues: 1016 helix: 2.30 (0.26), residues: 395 sheet: 0.01 (0.36), residues: 209 loop : -0.86 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE N 108 TYR 0.019 0.001 TYR A 339 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8415 (mttp) REVERT: A 392 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7528 (mm-30) REVERT: B 212 ASP cc_start: 0.7881 (t70) cc_final: 0.7459 (t70) REVERT: B 217 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7257 (pmt) REVERT: B 228 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7414 (p0) REVERT: B 270 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7962 (pp) REVERT: B 280 LYS cc_start: 0.8673 (tttm) cc_final: 0.8344 (ttpt) REVERT: G 21 MET cc_start: 0.7387 (tpt) cc_final: 0.6888 (mmm) REVERT: N 60 TYR cc_start: 0.8888 (m-80) cc_final: 0.8600 (m-80) REVERT: N 77 ASN cc_start: 0.7886 (m-40) cc_final: 0.7360 (t0) REVERT: R 146 TRP cc_start: 0.7059 (OUTLIER) cc_final: 0.6106 (m-10) outliers start: 26 outliers final: 15 residues processed: 124 average time/residue: 1.1141 time to fit residues: 147.5765 Evaluate side-chains 127 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 0.0770 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8259 Z= 0.191 Angle : 0.528 9.368 11232 Z= 0.259 Chirality : 0.042 0.198 1265 Planarity : 0.004 0.045 1428 Dihedral : 6.756 86.670 1332 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.45 % Allowed : 17.14 % Favored : 79.40 % 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: 0.91 (0.27), residues: 1016 helix: 2.33 (0.26), residues: 402 sheet: -0.06 (0.36), residues: 209 loop : -0.80 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE N 108 TYR 0.018 0.001 TYR A 339 ARG 0.013 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8350 (mtmt) REVERT: A 392 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7554 (mm-30) REVERT: B 35 ASN cc_start: 0.8260 (t0) cc_final: 0.8026 (t0) REVERT: B 212 ASP cc_start: 0.7902 (t70) cc_final: 0.7457 (t70) REVERT: B 217 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7324 (pmt) REVERT: B 228 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7406 (p0) REVERT: B 270 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7966 (pp) REVERT: B 280 LYS cc_start: 0.8661 (tttm) cc_final: 0.8343 (ttpt) REVERT: G 21 MET cc_start: 0.7334 (tpt) cc_final: 0.6808 (mmm) REVERT: N 5 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7306 (mm-40) REVERT: N 60 TYR cc_start: 0.8920 (m-80) cc_final: 0.8658 (m-80) REVERT: R 97 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7522 (mt) REVERT: R 146 TRP cc_start: 0.7063 (OUTLIER) cc_final: 0.6097 (m-10) REVERT: R 154 ASN cc_start: 0.8351 (m110) cc_final: 0.8012 (m-40) outliers start: 29 outliers final: 16 residues processed: 132 average time/residue: 1.0593 time to fit residues: 149.5422 Evaluate side-chains 130 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.0040 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 0.0270 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8259 Z= 0.137 Angle : 0.502 9.482 11232 Z= 0.244 Chirality : 0.041 0.190 1265 Planarity : 0.004 0.047 1428 Dihedral : 6.566 86.738 1332 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.38 % Allowed : 19.05 % Favored : 78.57 % 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: 1.17 (0.27), residues: 1016 helix: 2.56 (0.26), residues: 402 sheet: 0.15 (0.36), residues: 214 loop : -0.73 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 281 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE B 241 TYR 0.017 0.001 TYR N 95 ARG 0.012 0.000 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8357 (mtmt) REVERT: A 392 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7551 (mm-30) REVERT: B 14 LEU cc_start: 0.7932 (mt) cc_final: 0.7500 (mp) REVERT: B 35 ASN cc_start: 0.8167 (t0) cc_final: 0.7915 (t0) REVERT: B 212 ASP cc_start: 0.7907 (t70) cc_final: 0.7472 (t70) REVERT: B 215 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7055 (mm-30) REVERT: B 217 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7214 (pmt) REVERT: B 228 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7171 (p0) REVERT: B 270 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7961 (pp) REVERT: G 21 MET cc_start: 0.7380 (tpt) cc_final: 0.6817 (mmm) REVERT: N 59 SER cc_start: 0.7570 (OUTLIER) cc_final: 0.7297 (t) REVERT: N 60 TYR cc_start: 0.8924 (m-80) cc_final: 0.8629 (m-80) REVERT: N 77 ASN cc_start: 0.7850 (m-40) cc_final: 0.7325 (t0) REVERT: R 79 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7576 (mmt-90) REVERT: R 97 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7524 (mt) outliers start: 20 outliers final: 11 residues processed: 131 average time/residue: 1.0696 time to fit residues: 149.7980 Evaluate side-chains 129 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 149 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 39 GLN R 32 ASN R 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8259 Z= 0.257 Angle : 0.570 9.663 11232 Z= 0.282 Chirality : 0.044 0.204 1265 Planarity : 0.004 0.048 1428 Dihedral : 6.709 84.919 1332 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.86 % Allowed : 18.57 % Favored : 78.57 % 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: 0.96 (0.27), residues: 1016 helix: 2.47 (0.26), residues: 396 sheet: -0.18 (0.36), residues: 212 loop : -0.75 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.022 0.002 PHE N 108 TYR 0.020 0.001 TYR A 339 ARG 0.012 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.890 Fit side-chains REVERT: A 211 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8370 (mtmt) REVERT: A 392 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7574 (mm-30) REVERT: B 212 ASP cc_start: 0.7966 (t70) cc_final: 0.7476 (t70) REVERT: B 215 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7067 (mm-30) REVERT: B 217 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7313 (pmt) REVERT: B 228 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7407 (p0) REVERT: B 270 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7978 (pp) REVERT: G 21 MET cc_start: 0.7370 (tpt) cc_final: 0.6880 (mmm) REVERT: R 97 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7530 (mt) REVERT: R 146 TRP cc_start: 0.7070 (OUTLIER) cc_final: 0.6038 (m-10) REVERT: R 154 ASN cc_start: 0.8320 (m-40) cc_final: 0.7993 (m-40) outliers start: 24 outliers final: 13 residues processed: 126 average time/residue: 1.1927 time to fit residues: 160.5123 Evaluate side-chains 131 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 149 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 8 optimal weight: 0.0060 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8259 Z= 0.144 Angle : 0.516 9.713 11232 Z= 0.254 Chirality : 0.041 0.190 1265 Planarity : 0.004 0.052 1428 Dihedral : 6.579 85.601 1332 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.14 % Allowed : 19.76 % Favored : 78.10 % 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: 1.24 (0.27), residues: 1016 helix: 2.66 (0.26), residues: 401 sheet: 0.05 (0.36), residues: 217 loop : -0.65 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 281 HIS 0.002 0.001 HIS B 54 PHE 0.012 0.001 PHE B 241 TYR 0.017 0.001 TYR N 95 ARG 0.013 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.936 Fit side-chains REVERT: A 211 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8367 (mtmt) REVERT: A 392 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7564 (mm-30) REVERT: B 212 ASP cc_start: 0.7907 (t70) cc_final: 0.7521 (t70) REVERT: B 215 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7107 (mm-30) REVERT: B 217 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7281 (pmt) REVERT: B 228 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7309 (p0) REVERT: B 270 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7940 (pp) REVERT: G 21 MET cc_start: 0.7370 (tpt) cc_final: 0.6830 (mmm) REVERT: N 59 SER cc_start: 0.7561 (OUTLIER) cc_final: 0.7319 (t) REVERT: N 60 TYR cc_start: 0.8848 (m-80) cc_final: 0.8593 (m-80) REVERT: R 97 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7536 (mt) REVERT: R 154 ASN cc_start: 0.8335 (m-40) cc_final: 0.8002 (m-40) outliers start: 18 outliers final: 9 residues processed: 127 average time/residue: 1.2142 time to fit residues: 164.2209 Evaluate side-chains 128 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 149 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 0.0170 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111862 restraints weight = 17492.525| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.24 r_work: 0.3140 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8259 Z= 0.144 Angle : 0.509 9.670 11232 Z= 0.249 Chirality : 0.041 0.190 1265 Planarity : 0.004 0.054 1428 Dihedral : 6.459 85.117 1332 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.67 % Allowed : 20.36 % Favored : 77.98 % 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: 1.42 (0.27), residues: 1016 helix: 2.76 (0.26), residues: 401 sheet: 0.25 (0.35), residues: 221 loop : -0.55 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 281 HIS 0.002 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.017 0.001 TYR N 95 ARG 0.013 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3232.15 seconds wall clock time: 58 minutes 1.64 seconds (3481.64 seconds total)