Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 00:29:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2h_25613/04_2023/7t2h_25613_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2h_25613/04_2023/7t2h_25613.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2h_25613/04_2023/7t2h_25613_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/7t2h_25613/04_2023/7t2h_25613_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2h_25613/04_2023/7t2h_25613_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2h_25613/04_2023/7t2h_25613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2h_25613/04_2023/7t2h_25613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2h_25613/04_2023/7t2h_25613_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t2h_25613/04_2023/7t2h_25613_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 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 66 5.16 5 C 5537 2.51 5 N 1470 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8677 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1720 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2564 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 405 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1761 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2227 Unusual residues: {'EID': 1} Classifications: {'peptide': 281, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270, None: 1} Not linked: pdbres="ARG D 345 " pdbres="EID D 401 " Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 5.09, per 1000 atoms: 0.59 Number of scatterers: 8677 At special positions: 0 Unit cell: (96.46, 118.72, 112.36, 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 66 16.00 O 1604 8.00 N 1470 7.00 C 5537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " 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: 3.39 Conformation dependent library (CDL) restraints added in 1.5 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 15 sheets defined 33.2% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.610A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.783A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.031A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 6 through 24 removed outlier: 3.793A pdb=" N GLU B 12 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 13 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.744A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'D' and resid 67 through 95 Processing helix chain 'D' and resid 102 through 130 removed outlier: 4.336A pdb=" N THR D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 138 through 170 Processing helix chain 'D' and resid 172 through 178 removed outlier: 4.625A pdb=" N ASP D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 204 removed outlier: 4.101A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 229 through 240 removed outlier: 3.846A pdb=" N LYS D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 261 removed outlier: 4.285A pdb=" N SER D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 269 through 305 Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 312 through 336 removed outlier: 4.037A pdb=" N VAL D 316 " --> pdb=" O THR D 312 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'D' and resid 341 through 343 No H-bonds generated for 'chain 'D' and resid 341 through 343' Processing sheet with id= A, first strand: chain 'A' and resid 33 through 38 removed outlier: 6.450A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 220 through 226 removed outlier: 6.902A pdb=" N SER A 263 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE A 223 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.758A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.664A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.580A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 198 through 201 removed outlier: 3.599A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 249 through 252 removed outlier: 3.586A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.510A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.702A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.433A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.606A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 92 through 99 removed outlier: 5.929A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.194A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 143 through 147 removed outlier: 3.546A pdb=" N THR E 201 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 206 through 210 364 hydrogen bonds defined for protein. 1020 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: 2.59 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1396 1.31 - 1.44: 2442 1.44 - 1.57: 4920 1.57 - 1.70: 1 1.70 - 1.82: 98 Bond restraints: 8857 Sorted by residual: bond pdb=" C14 EID D 401 " pdb=" N15 EID D 401 " ideal model delta sigma weight residual 1.498 1.430 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C12 EID D 401 " pdb=" C27 EID D 401 " ideal model delta sigma weight residual 1.589 1.528 0.061 2.00e-02 2.50e+03 9.18e+00 bond pdb=" C16 EID D 401 " pdb=" N15 EID D 401 " ideal model delta sigma weight residual 1.493 1.434 0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" C13 EID D 401 " pdb=" C14 EID D 401 " ideal model delta sigma weight residual 1.542 1.491 0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" C06 EID D 401 " pdb=" N05 EID D 401 " ideal model delta sigma weight residual 1.501 1.458 0.043 2.00e-02 2.50e+03 4.68e+00 ... (remaining 8852 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.40: 189 106.40 - 113.31: 4861 113.31 - 120.23: 3168 120.23 - 127.14: 3701 127.14 - 134.06: 88 Bond angle restraints: 12007 Sorted by residual: angle pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " ideal model delta sigma weight residual 114.40 123.02 -8.62 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 121.76 -7.36 2.30e+00 1.89e-01 1.02e+01 angle pdb=" N LEU D 121 " pdb=" CA LEU D 121 " pdb=" C LEU D 121 " ideal model delta sigma weight residual 109.81 114.24 -4.43 2.21e+00 2.05e-01 4.01e+00 angle pdb=" C13 EID D 401 " pdb=" C14 EID D 401 " pdb=" N15 EID D 401 " ideal model delta sigma weight residual 112.09 106.11 5.98 3.00e+00 1.11e-01 3.97e+00 angle pdb=" N ASN D 332 " pdb=" CA ASN D 332 " pdb=" C ASN D 332 " ideal model delta sigma weight residual 109.81 114.20 -4.39 2.21e+00 2.05e-01 3.95e+00 ... (remaining 12002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4714 17.52 - 35.03: 433 35.03 - 52.55: 80 52.55 - 70.06: 16 70.06 - 87.58: 6 Dihedral angle restraints: 5249 sinusoidal: 1999 harmonic: 3250 Sorted by residual: dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASP B 298 " pdb=" CB ASP B 298 " pdb=" CG ASP B 298 " pdb=" OD1 ASP B 298 " ideal model delta sinusoidal sigma weight residual -30.00 -84.32 54.32 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA TYR B 111 " pdb=" C TYR B 111 " pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 5246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.090: 1374 1.090 - 2.180: 0 2.180 - 3.270: 0 3.270 - 4.360: 0 4.360 - 5.449: 1 Chirality restraints: 1375 Sorted by residual: chirality pdb=" C12 EID D 401 " pdb=" C13 EID D 401 " pdb=" C25 EID D 401 " pdb=" C27 EID D 401 " both_signs ideal model delta sigma weight residual False -2.70 2.75 -5.45 2.00e-01 2.50e+01 7.42e+02 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1372 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 332 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO D 333 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 333 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 333 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 121 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO D 122 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 122 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 122 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 78 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C VAL D 78 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL D 78 " -0.008 2.00e-02 2.50e+03 pdb=" N CYS D 79 " -0.007 2.00e-02 2.50e+03 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 309 2.71 - 3.25: 8646 3.25 - 3.80: 13801 3.80 - 4.35: 17787 4.35 - 4.90: 31197 Nonbonded interactions: 71740 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.158 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.220 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.243 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.270 2.440 ... (remaining 71735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 4.280 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.180 Find NCS groups from input model: 0.250 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 8857 Z= 0.255 Angle : 0.521 8.617 12007 Z= 0.288 Chirality : 0.153 5.449 1375 Planarity : 0.003 0.040 1512 Dihedral : 14.115 87.579 3139 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.23), residues: 1103 helix: -0.72 (0.25), residues: 377 sheet: -3.31 (0.24), residues: 270 loop : -2.38 (0.26), residues: 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 166 average time/residue: 0.2517 time to fit residues: 55.0332 Evaluate side-chains 130 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0822 time to fit residues: 1.5542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.0170 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 213 HIS A 269 ASN A 306 GLN A 333 GLN B 13 GLN B 17 GLN B 44 GLN B 91 HIS B 110 ASN B 119 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN E 39 GLN E 82 GLN E 167 GLN E 171 GLN D 124 GLN D 328 ASN D 332 ASN D 342 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 8857 Z= 0.170 Angle : 0.623 25.362 12007 Z= 0.291 Chirality : 0.090 2.954 1375 Planarity : 0.003 0.031 1512 Dihedral : 4.892 85.800 1215 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.25), residues: 1103 helix: 0.52 (0.28), residues: 362 sheet: -2.88 (0.24), residues: 296 loop : -1.64 (0.29), residues: 445 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.069 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 156 average time/residue: 0.2361 time to fit residues: 50.4056 Evaluate side-chains 133 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0878 time to fit residues: 2.7196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 100 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN D 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 8857 Z= 0.211 Angle : 0.639 26.093 12007 Z= 0.296 Chirality : 0.088 2.887 1375 Planarity : 0.003 0.028 1512 Dihedral : 4.595 67.945 1215 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.25), residues: 1103 helix: 0.88 (0.28), residues: 357 sheet: -2.58 (0.25), residues: 290 loop : -1.37 (0.29), residues: 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 0.952 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 152 average time/residue: 0.2279 time to fit residues: 47.5160 Evaluate side-chains 141 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1319 time to fit residues: 3.6705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 8857 Z= 0.220 Angle : 0.643 26.185 12007 Z= 0.298 Chirality : 0.088 2.874 1375 Planarity : 0.003 0.032 1512 Dihedral : 4.394 52.962 1215 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.25), residues: 1103 helix: 1.04 (0.28), residues: 363 sheet: -2.43 (0.25), residues: 294 loop : -1.21 (0.30), residues: 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.028 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 141 average time/residue: 0.2370 time to fit residues: 45.1608 Evaluate side-chains 131 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0829 time to fit residues: 2.1631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.0670 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 8857 Z= 0.240 Angle : 0.652 26.185 12007 Z= 0.303 Chirality : 0.088 2.873 1375 Planarity : 0.003 0.029 1512 Dihedral : 4.290 38.884 1215 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1103 helix: 1.02 (0.28), residues: 363 sheet: -2.36 (0.26), residues: 294 loop : -1.14 (0.30), residues: 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.031 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 138 average time/residue: 0.2373 time to fit residues: 44.2934 Evaluate side-chains 130 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1403 time to fit residues: 3.0918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 8 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 8857 Z= 0.186 Angle : 0.630 26.387 12007 Z= 0.291 Chirality : 0.087 2.860 1375 Planarity : 0.003 0.031 1512 Dihedral : 4.138 29.846 1215 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 1103 helix: 1.18 (0.28), residues: 363 sheet: -2.17 (0.26), residues: 292 loop : -1.11 (0.30), residues: 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 0.943 Fit side-chains outliers start: 11 outliers final: 2 residues processed: 137 average time/residue: 0.2277 time to fit residues: 42.6240 Evaluate side-chains 127 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0792 time to fit residues: 1.6888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 8857 Z= 0.174 Angle : 0.638 26.445 12007 Z= 0.291 Chirality : 0.087 2.856 1375 Planarity : 0.003 0.032 1512 Dihedral : 4.041 29.075 1215 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1103 helix: 1.28 (0.28), residues: 363 sheet: -2.03 (0.26), residues: 291 loop : -1.00 (0.29), residues: 449 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.027 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 137 average time/residue: 0.2409 time to fit residues: 44.3437 Evaluate side-chains 132 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0808 time to fit residues: 1.8874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 8857 Z= 0.190 Angle : 0.640 26.401 12007 Z= 0.292 Chirality : 0.087 2.858 1375 Planarity : 0.003 0.032 1512 Dihedral : 4.003 28.839 1215 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.25), residues: 1103 helix: 1.27 (0.28), residues: 363 sheet: -1.94 (0.26), residues: 292 loop : -0.94 (0.29), residues: 448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.078 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 135 average time/residue: 0.2403 time to fit residues: 43.6116 Evaluate side-chains 129 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2308 time to fit residues: 2.1836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.0970 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 8857 Z= 0.206 Angle : 0.652 26.346 12007 Z= 0.298 Chirality : 0.088 2.859 1375 Planarity : 0.003 0.033 1512 Dihedral : 4.024 28.596 1215 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1103 helix: 1.25 (0.28), residues: 363 sheet: -1.93 (0.27), residues: 294 loop : -0.88 (0.30), residues: 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.973 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 130 average time/residue: 0.2466 time to fit residues: 43.2389 Evaluate side-chains 129 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0863 time to fit residues: 1.6366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.1980 chunk 72 optimal weight: 0.0870 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 9 optimal weight: 0.1980 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 overall best weight: 0.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.073 8857 Z= 0.146 Angle : 0.627 26.621 12007 Z= 0.284 Chirality : 0.087 2.843 1375 Planarity : 0.003 0.033 1512 Dihedral : 3.861 29.144 1215 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.26), residues: 1103 helix: 1.39 (0.28), residues: 364 sheet: -1.75 (0.27), residues: 290 loop : -0.86 (0.29), residues: 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.001 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 138 average time/residue: 0.2277 time to fit residues: 43.3620 Evaluate side-chains 136 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0875 time to fit residues: 1.5937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.171284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128397 restraints weight = 9393.990| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.24 r_work: 0.2973 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 8857 Z= 0.237 Angle : 0.675 26.269 12007 Z= 0.308 Chirality : 0.088 2.861 1375 Planarity : 0.003 0.042 1512 Dihedral : 4.005 29.945 1215 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1103 helix: 1.32 (0.28), residues: 364 sheet: -1.69 (0.27), residues: 291 loop : -0.86 (0.30), residues: 448 =============================================================================== Job complete usr+sys time: 2143.50 seconds wall clock time: 39 minutes 38.81 seconds (2378.81 seconds total)