Starting phenix.real_space_refine on Thu Mar 14 16:13:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbi_31880/03_2024/7vbi_31880_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbi_31880/03_2024/7vbi_31880.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/7vbi_31880/03_2024/7vbi_31880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbi_31880/03_2024/7vbi_31880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbi_31880/03_2024/7vbi_31880_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbi_31880/03_2024/7vbi_31880_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= -0.001 sd= 0.108 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 54 5.16 5 C 5882 2.51 5 N 1596 2.21 5 O 1691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "P TYR 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 9": "OD1" <-> "OD2" Residue "P ASP 15": "OD1" <-> "OD2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R GLU 52": "OE1" <-> "OE2" Residue "R ASP 53": "OD1" <-> "OD2" Residue "R PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R GLU 125": "OE1" <-> "OE2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 198": "OD1" <-> "OD2" Residue "R ASP 215": "OD1" <-> "OD2" Residue "R TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 293": "OD1" <-> "OD2" Residue "R GLU 294": "OE1" <-> "OE2" Residue "R ARG 326": "NH1" <-> "NH2" Residue "R GLU 373": "OE1" <-> "OE2" Residue "R PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 414": "NH1" <-> "NH2" Residue "R GLU 418": "OE1" <-> "OE2" Residue "R ARG 421": "NH1" <-> "NH2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "G ASP 26": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9223 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1891 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3115 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Time building chain proxies: 5.30, per 1000 atoms: 0.57 Number of scatterers: 9223 At special positions: 0 Unit cell: (76.041, 100.674, 173.502, 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 54 16.00 O 1691 8.00 N 1596 7.00 C 5882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.04 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 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: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 11 sheets defined 36.3% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.582A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.690A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.646A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) 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: 3.631A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'P' and resid 4 through 28 removed outlier: 3.669A pdb=" N VAL P 23 " --> pdb=" O GLN P 19 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 52 removed outlier: 3.577A pdb=" N TYR R 42 " --> pdb=" O LYS R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 168 Processing helix chain 'R' and resid 175 through 204 removed outlier: 3.725A pdb=" N PHE R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 213 Processing helix chain 'R' and resid 220 through 222 No H-bonds generated for 'chain 'R' and resid 220 through 222' Processing helix chain 'R' and resid 224 through 255 removed outlier: 3.542A pdb=" N VAL R 237 " --> pdb=" O MET R 233 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 274 removed outlier: 3.761A pdb=" N SER R 271 " --> pdb=" O ARG R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 279 No H-bonds generated for 'chain 'R' and resid 276 through 279' Processing helix chain 'R' and resid 282 through 290 Processing helix chain 'R' and resid 294 through 297 removed outlier: 3.691A pdb=" N TRP R 297 " --> pdb=" O GLU R 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 294 through 297' Processing helix chain 'R' and resid 307 through 335 Proline residue: R 312 - end of helix removed outlier: 3.663A pdb=" N ALA R 316 " --> pdb=" O PRO R 312 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N CYS R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 365 No H-bonds generated for 'chain 'R' and resid 363 through 365' Processing helix chain 'R' and resid 378 through 388 Processing helix chain 'R' and resid 391 through 402 removed outlier: 3.635A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 421 removed outlier: 3.962A pdb=" N GLU R 412 " --> pdb=" O GLU R 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.882A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'G' and resid 7 through 21 removed outlier: 3.794A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.261A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.626A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.396A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'R' and resid 81 through 83 removed outlier: 4.285A pdb=" N VAL R 81 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS R 104 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL R 83 " --> pdb=" O ARG R 102 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG R 102 " --> pdb=" O VAL R 83 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.006A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.928A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.732A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.642A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= J, first strand: chain 'B' and resid 295 through 298 removed outlier: 4.063A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.475A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1107 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: 2.47 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2583 1.33 - 1.46: 2487 1.46 - 1.58: 4288 1.58 - 1.71: 0 1.71 - 1.84: 73 Bond restraints: 9431 Sorted by residual: bond pdb=" C PHE B 234 " pdb=" N PHE B 235 " ideal model delta sigma weight residual 1.328 1.274 0.054 1.44e-02 4.82e+03 1.41e+01 bond pdb=" CA PHE A 238 " pdb=" CB PHE A 238 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.51e-02 4.39e+03 1.33e+01 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.398 0.115 3.90e-02 6.57e+02 8.62e+00 bond pdb=" C PHE B 235 " pdb=" N PRO B 236 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 6.91e+00 ... (remaining 9426 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.22: 195 106.22 - 113.24: 5007 113.24 - 120.27: 3655 120.27 - 127.29: 3808 127.29 - 134.31: 122 Bond angle restraints: 12787 Sorted by residual: angle pdb=" C THR A 319 " pdb=" N THR A 320 " pdb=" CA THR A 320 " ideal model delta sigma weight residual 120.51 130.15 -9.64 1.45e+00 4.76e-01 4.42e+01 angle pdb=" O ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " ideal model delta sigma weight residual 122.39 129.37 -6.98 1.29e+00 6.01e-01 2.93e+01 angle pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta sigma weight residual 120.39 127.58 -7.19 1.39e+00 5.18e-01 2.67e+01 angle pdb=" C ARG N 98 " pdb=" N CYS N 99 " pdb=" CA CYS N 99 " ideal model delta sigma weight residual 122.74 110.14 12.60 2.44e+00 1.68e-01 2.67e+01 angle pdb=" N VAL R 405 " pdb=" CA VAL R 405 " pdb=" C VAL R 405 " ideal model delta sigma weight residual 113.10 108.34 4.76 9.70e-01 1.06e+00 2.41e+01 ... (remaining 12782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 4972 18.13 - 36.25: 488 36.25 - 54.38: 83 54.38 - 72.50: 21 72.50 - 90.63: 9 Dihedral angle restraints: 5573 sinusoidal: 2202 harmonic: 3371 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 162.50 -69.50 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -144.63 -35.37 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA LEU R 217 " pdb=" C LEU R 217 " pdb=" N LEU R 218 " pdb=" CA LEU R 218 " ideal model delta harmonic sigma weight residual 180.00 146.84 33.16 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 5570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 873 0.050 - 0.101: 396 0.101 - 0.151: 110 0.151 - 0.201: 23 0.201 - 0.251: 10 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CB ILE N 51 " pdb=" CA ILE N 51 " pdb=" CG1 ILE N 51 " pdb=" CG2 ILE N 51 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE A 308 " pdb=" CA ILE A 308 " pdb=" CG1 ILE A 308 " pdb=" CG2 ILE A 308 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA VAL R 282 " pdb=" N VAL R 282 " pdb=" C VAL R 282 " pdb=" CB VAL R 282 " both_signs ideal model delta sigma weight residual False 2.44 2.21 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1409 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 384 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU R 384 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU R 384 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE R 385 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 55 " -0.051 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO R 56 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 56 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 56 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 395 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C GLY R 395 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY R 395 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU R 396 " -0.017 2.00e-02 2.50e+03 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 753 2.73 - 3.27: 8471 3.27 - 3.81: 14957 3.81 - 4.36: 18534 4.36 - 4.90: 32146 Nonbonded interactions: 74861 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.181 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.265 2.440 nonbonded pdb=" O TYR R 69 " pdb=" OH TYR R 88 " model vdw 2.267 2.440 nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.290 2.520 nonbonded pdb=" OE2 GLU P 3 " pdb=" OH TYR R 152 " model vdw 2.315 2.440 ... (remaining 74856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 4.070 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 27.750 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.011 0.115 9431 Z= 0.731 Angle : 1.125 12.808 12787 Z= 0.633 Chirality : 0.063 0.251 1412 Planarity : 0.008 0.076 1623 Dihedral : 14.914 90.630 3377 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.81 % Allowed : 7.42 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % 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: -3.46 (0.20), residues: 1133 helix: -2.64 (0.18), residues: 429 sheet: -1.08 (0.32), residues: 229 loop : -2.44 (0.23), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP R 72 HIS 0.020 0.003 HIS A 357 PHE 0.044 0.004 PHE N 108 TYR 0.027 0.003 TYR R 148 ARG 0.014 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 0.961 Fit side-chains REVERT: A 272 LEU cc_start: 0.8286 (mt) cc_final: 0.8052 (mm) REVERT: A 339 TYR cc_start: 0.8678 (m-80) cc_final: 0.8439 (m-80) REVERT: N 34 MET cc_start: 0.8108 (mmm) cc_final: 0.7733 (mmm) REVERT: N 46 GLU cc_start: 0.7187 (mp0) cc_final: 0.6890 (mp0) REVERT: N 94 TYR cc_start: 0.8429 (m-80) cc_final: 0.8141 (m-80) REVERT: N 95 TYR cc_start: 0.8513 (m-80) cc_final: 0.8165 (m-80) REVERT: P 9 ASP cc_start: 0.8069 (m-30) cc_final: 0.7473 (m-30) REVERT: R 146 ILE cc_start: 0.8759 (mt) cc_final: 0.8484 (mp) REVERT: R 267 ARG cc_start: 0.7041 (tpt170) cc_final: 0.6324 (mpp80) REVERT: R 336 LYS cc_start: 0.8081 (mttp) cc_final: 0.7778 (mmtm) REVERT: R 348 ARG cc_start: 0.7395 (tpm170) cc_final: 0.6602 (mtp180) REVERT: R 376 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7274 (mtt90) REVERT: R 415 LYS cc_start: 0.7048 (mtmt) cc_final: 0.6697 (mttt) REVERT: B 42 ARG cc_start: 0.7356 (ttp-110) cc_final: 0.7059 (ttm-80) outliers start: 8 outliers final: 4 residues processed: 177 average time/residue: 1.3074 time to fit residues: 245.6602 Evaluate side-chains 135 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 14 ASN A 23 ASN A 35 GLN A 227 GLN A 279 ASN A 371 ASN N 1 GLN N 74 ASN N 77 ASN R 37 GLN R 45 GLN R 140 GLN R 211 GLN ** R 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 GLN B 88 ASN B 119 ASN B 132 ASN B 230 ASN B 239 ASN B 340 ASN G 24 ASN G 59 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9431 Z= 0.188 Angle : 0.590 9.433 12787 Z= 0.314 Chirality : 0.041 0.160 1412 Planarity : 0.005 0.073 1623 Dihedral : 5.816 47.828 1273 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.56 % Allowed : 14.02 % Favored : 82.42 % 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: -1.83 (0.23), residues: 1133 helix: -0.67 (0.23), residues: 435 sheet: -0.54 (0.32), residues: 233 loop : -2.02 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.022 0.001 TYR R 148 ARG 0.006 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 1.046 Fit side-chains REVERT: A 60 MET cc_start: 0.8456 (mmp) cc_final: 0.8255 (mmm) REVERT: A 272 LEU cc_start: 0.8107 (mt) cc_final: 0.7839 (mm) REVERT: A 344 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6965 (tp30) REVERT: N 46 GLU cc_start: 0.7252 (mp0) cc_final: 0.6942 (mp0) REVERT: P 3 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7194 (mm-30) REVERT: R 146 ILE cc_start: 0.8785 (mt) cc_final: 0.8562 (mp) REVERT: R 167 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7836 (pp) REVERT: R 202 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7453 (tttp) REVERT: R 267 ARG cc_start: 0.7023 (tpt170) cc_final: 0.6275 (mpp80) REVERT: R 336 LYS cc_start: 0.7947 (mttp) cc_final: 0.7644 (mmtm) REVERT: R 376 ARG cc_start: 0.7827 (ptp-170) cc_final: 0.7190 (mtt90) REVERT: R 387 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5600 (mt-10) REVERT: B 70 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8508 (pt) REVERT: B 111 TYR cc_start: 0.8581 (m-80) cc_final: 0.8356 (m-10) REVERT: B 186 ASP cc_start: 0.8048 (m-30) cc_final: 0.7706 (m-30) REVERT: G 21 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.5233 (tmm) outliers start: 35 outliers final: 12 residues processed: 166 average time/residue: 1.2118 time to fit residues: 214.6318 Evaluate side-chains 152 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 100 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 279 ASN A 387 HIS N 77 ASN R 394 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9431 Z= 0.231 Angle : 0.585 9.192 12787 Z= 0.311 Chirality : 0.041 0.182 1412 Planarity : 0.004 0.073 1623 Dihedral : 5.495 46.926 1269 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.17 % Allowed : 15.75 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.19 (0.24), residues: 1133 helix: 0.22 (0.25), residues: 432 sheet: -0.44 (0.32), residues: 247 loop : -1.94 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE N 108 TYR 0.022 0.001 TYR R 148 ARG 0.006 0.000 ARG R 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7407 (pp20) REVERT: A 272 LEU cc_start: 0.8049 (mt) cc_final: 0.7814 (mm) REVERT: A 343 ASP cc_start: 0.6943 (m-30) cc_final: 0.6570 (t0) REVERT: A 386 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7588 (ttm) REVERT: N 46 GLU cc_start: 0.7235 (mp0) cc_final: 0.6939 (mp0) REVERT: P 3 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: R 146 ILE cc_start: 0.8758 (mt) cc_final: 0.8530 (mp) REVERT: R 167 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7771 (pp) REVERT: R 202 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7443 (tttp) REVERT: R 267 ARG cc_start: 0.6977 (tpt170) cc_final: 0.6283 (mpp80) REVERT: R 336 LYS cc_start: 0.7922 (mttp) cc_final: 0.7686 (mmtm) REVERT: R 348 ARG cc_start: 0.7484 (tpm-80) cc_final: 0.6325 (mtp180) REVERT: R 376 ARG cc_start: 0.7779 (ptp-170) cc_final: 0.7160 (mtt90) REVERT: R 387 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5665 (mt-10) REVERT: B 70 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8540 (pt) REVERT: B 111 TYR cc_start: 0.8584 (m-80) cc_final: 0.8344 (m-10) REVERT: B 171 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8251 (mm) REVERT: B 186 ASP cc_start: 0.8035 (m-30) cc_final: 0.7627 (m-30) REVERT: G 21 MET cc_start: 0.5564 (OUTLIER) cc_final: 0.5268 (tmm) outliers start: 41 outliers final: 17 residues processed: 166 average time/residue: 1.1656 time to fit residues: 207.0608 Evaluate side-chains 154 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 77 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9431 Z= 0.346 Angle : 0.640 11.329 12787 Z= 0.338 Chirality : 0.044 0.186 1412 Planarity : 0.005 0.075 1623 Dihedral : 5.631 58.325 1269 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.88 % Allowed : 16.46 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.24), residues: 1133 helix: 0.60 (0.25), residues: 425 sheet: -0.24 (0.33), residues: 235 loop : -1.90 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE N 108 TYR 0.025 0.002 TYR R 148 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 137 time to evaluate : 0.968 Fit side-chains REVERT: A 15 GLU cc_start: 0.6098 (tt0) cc_final: 0.5659 (tt0) REVERT: A 272 LEU cc_start: 0.8118 (mt) cc_final: 0.7899 (mp) REVERT: A 283 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7072 (mtm110) REVERT: A 343 ASP cc_start: 0.7020 (m-30) cc_final: 0.6648 (t0) REVERT: A 386 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7664 (ttm) REVERT: N 46 GLU cc_start: 0.7138 (mp0) cc_final: 0.6722 (mp0) REVERT: P 3 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7138 (mm-30) REVERT: R 146 ILE cc_start: 0.8797 (mt) cc_final: 0.8565 (mp) REVERT: R 167 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7919 (pp) REVERT: R 202 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7462 (tttp) REVERT: R 267 ARG cc_start: 0.7004 (tpt170) cc_final: 0.6310 (mpp80) REVERT: R 303 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7495 (mtt) REVERT: R 336 LYS cc_start: 0.7934 (mttp) cc_final: 0.7670 (mmtm) REVERT: R 348 ARG cc_start: 0.7573 (tpm-80) cc_final: 0.6382 (mtp180) REVERT: R 376 ARG cc_start: 0.7746 (ptp-170) cc_final: 0.7151 (mtt90) REVERT: R 387 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5745 (mt-10) REVERT: B 70 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8632 (pt) REVERT: B 100 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 111 TYR cc_start: 0.8601 (m-80) cc_final: 0.8365 (m-10) REVERT: B 171 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8298 (mm) REVERT: B 186 ASP cc_start: 0.8068 (m-30) cc_final: 0.7567 (m-30) REVERT: B 279 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8467 (t) REVERT: G 21 MET cc_start: 0.5552 (OUTLIER) cc_final: 0.5227 (tmm) outliers start: 48 outliers final: 23 residues processed: 166 average time/residue: 1.1723 time to fit residues: 208.2332 Evaluate side-chains 161 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 19 GLN Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN N 77 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9431 Z= 0.316 Angle : 0.617 9.502 12787 Z= 0.326 Chirality : 0.043 0.155 1412 Planarity : 0.005 0.076 1623 Dihedral : 5.528 55.792 1269 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.28 % Allowed : 18.09 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.75 (0.24), residues: 1133 helix: 0.76 (0.25), residues: 426 sheet: -0.24 (0.32), residues: 237 loop : -1.82 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.020 0.002 PHE N 108 TYR 0.022 0.002 TYR R 148 ARG 0.009 0.000 ARG R 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 131 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6209 (tt0) cc_final: 0.5775 (tt0) REVERT: A 216 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7992 (mttp) REVERT: A 272 LEU cc_start: 0.8110 (mt) cc_final: 0.7895 (mp) REVERT: A 283 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7060 (mtm110) REVERT: A 386 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7650 (ttm) REVERT: N 46 GLU cc_start: 0.7149 (mp0) cc_final: 0.6900 (mp0) REVERT: R 146 ILE cc_start: 0.8800 (mt) cc_final: 0.8568 (mp) REVERT: R 167 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7969 (pp) REVERT: R 202 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7469 (tttp) REVERT: R 267 ARG cc_start: 0.7010 (tpt170) cc_final: 0.6314 (mpp80) REVERT: R 303 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7455 (mtt) REVERT: R 336 LYS cc_start: 0.7937 (mttp) cc_final: 0.7662 (mmtm) REVERT: R 348 ARG cc_start: 0.7597 (tpm-80) cc_final: 0.6367 (mtp180) REVERT: R 376 ARG cc_start: 0.7730 (ptp-170) cc_final: 0.7117 (mtt90) REVERT: R 387 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.5872 (mt-10) REVERT: B 70 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8622 (pt) REVERT: B 100 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 111 TYR cc_start: 0.8573 (m-80) cc_final: 0.8346 (m-10) REVERT: B 171 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8305 (mm) REVERT: B 186 ASP cc_start: 0.8058 (m-30) cc_final: 0.7583 (m-30) REVERT: G 21 MET cc_start: 0.5369 (OUTLIER) cc_final: 0.5048 (tmm) outliers start: 52 outliers final: 26 residues processed: 166 average time/residue: 1.1675 time to fit residues: 207.3819 Evaluate side-chains 166 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 19 GLN Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 82 ASN Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 37 GLN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9431 Z= 0.214 Angle : 0.557 7.095 12787 Z= 0.295 Chirality : 0.041 0.162 1412 Planarity : 0.004 0.078 1623 Dihedral : 5.276 53.725 1269 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.98 % Allowed : 19.11 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.43 (0.24), residues: 1133 helix: 1.06 (0.26), residues: 426 sheet: 0.04 (0.32), residues: 234 loop : -1.74 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE N 108 TYR 0.018 0.001 TYR R 148 ARG 0.009 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 139 time to evaluate : 1.040 Fit side-chains REVERT: A 272 LEU cc_start: 0.8069 (mt) cc_final: 0.7860 (mp) REVERT: A 386 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7564 (ttm) REVERT: N 46 GLU cc_start: 0.7175 (mp0) cc_final: 0.6889 (mp0) REVERT: P 3 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7039 (mm-30) REVERT: R 146 ILE cc_start: 0.8747 (mt) cc_final: 0.8520 (mp) REVERT: R 167 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7799 (pp) REVERT: R 202 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7462 (tttp) REVERT: R 267 ARG cc_start: 0.6987 (tpt170) cc_final: 0.6319 (mpp80) REVERT: R 336 LYS cc_start: 0.7917 (mttp) cc_final: 0.7652 (mmtm) REVERT: R 348 ARG cc_start: 0.7555 (tpm-80) cc_final: 0.6358 (mtp180) REVERT: R 376 ARG cc_start: 0.7645 (ptp-170) cc_final: 0.7048 (mtt90) REVERT: R 383 LYS cc_start: 0.8582 (tttm) cc_final: 0.8285 (tttp) REVERT: R 387 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5814 (mt-10) REVERT: B 70 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8535 (pt) REVERT: B 100 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8786 (p) REVERT: B 186 ASP cc_start: 0.8033 (m-30) cc_final: 0.7488 (m-30) REVERT: G 21 MET cc_start: 0.5237 (OUTLIER) cc_final: 0.5001 (tmm) outliers start: 49 outliers final: 21 residues processed: 168 average time/residue: 1.0840 time to fit residues: 195.7453 Evaluate side-chains 160 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9431 Z= 0.231 Angle : 0.567 7.396 12787 Z= 0.300 Chirality : 0.042 0.162 1412 Planarity : 0.004 0.078 1623 Dihedral : 5.217 53.184 1269 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.07 % Allowed : 20.93 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.32 (0.25), residues: 1133 helix: 1.15 (0.26), residues: 427 sheet: 0.09 (0.32), residues: 236 loop : -1.68 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.022 0.001 PHE B 292 TYR 0.019 0.001 TYR R 148 ARG 0.010 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 137 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8071 (mt) cc_final: 0.7860 (mp) REVERT: A 283 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6961 (mtm110) REVERT: A 386 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7574 (ttm) REVERT: N 46 GLU cc_start: 0.7178 (mp0) cc_final: 0.6912 (mp0) REVERT: P 3 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: R 41 GLU cc_start: 0.8361 (pp20) cc_final: 0.8015 (pp20) REVERT: R 146 ILE cc_start: 0.8746 (mt) cc_final: 0.8489 (mp) REVERT: R 167 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7775 (pp) REVERT: R 202 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7485 (tttp) REVERT: R 267 ARG cc_start: 0.6978 (tpt170) cc_final: 0.6315 (mpp80) REVERT: R 294 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6663 (pp20) REVERT: R 336 LYS cc_start: 0.7908 (mttp) cc_final: 0.7647 (mmtm) REVERT: R 348 ARG cc_start: 0.7569 (tpm-80) cc_final: 0.6378 (mtp180) REVERT: R 376 ARG cc_start: 0.7674 (ptp-170) cc_final: 0.7074 (mtt90) REVERT: R 383 LYS cc_start: 0.8586 (tttm) cc_final: 0.8296 (tttp) REVERT: R 387 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.5823 (mt-10) REVERT: B 70 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8509 (pt) REVERT: B 130 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6189 (pm20) REVERT: B 186 ASP cc_start: 0.8080 (m-30) cc_final: 0.7565 (m-30) REVERT: G 21 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.5012 (tmm) outliers start: 40 outliers final: 23 residues processed: 160 average time/residue: 1.1338 time to fit residues: 194.4554 Evaluate side-chains 158 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 19 GLN Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.0770 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9431 Z= 0.186 Angle : 0.536 7.323 12787 Z= 0.284 Chirality : 0.040 0.168 1412 Planarity : 0.004 0.079 1623 Dihedral : 5.007 52.205 1269 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.76 % Allowed : 21.44 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.15 (0.25), residues: 1133 helix: 1.30 (0.26), residues: 432 sheet: 0.19 (0.33), residues: 236 loop : -1.65 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE B 292 TYR 0.018 0.001 TYR R 148 ARG 0.009 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8051 (mt) cc_final: 0.7848 (mp) REVERT: A 283 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6979 (mtm110) REVERT: A 343 ASP cc_start: 0.6937 (m-30) cc_final: 0.6611 (m-30) REVERT: N 46 GLU cc_start: 0.7247 (mp0) cc_final: 0.6945 (mp0) REVERT: P 3 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: R 146 ILE cc_start: 0.8724 (mt) cc_final: 0.8460 (mp) REVERT: R 267 ARG cc_start: 0.6940 (tpt170) cc_final: 0.6299 (mpp80) REVERT: R 336 LYS cc_start: 0.7915 (mttp) cc_final: 0.7646 (mmtm) REVERT: R 348 ARG cc_start: 0.7508 (tpm-80) cc_final: 0.6341 (mtp180) REVERT: R 376 ARG cc_start: 0.7628 (ptp-170) cc_final: 0.7018 (mtt90) REVERT: R 383 LYS cc_start: 0.8583 (tttm) cc_final: 0.8343 (tttp) REVERT: R 387 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5795 (mt-10) REVERT: R 418 GLU cc_start: 0.7096 (tp30) cc_final: 0.6725 (tm-30) REVERT: B 70 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8443 (pt) REVERT: B 186 ASP cc_start: 0.8065 (m-30) cc_final: 0.7504 (m-30) outliers start: 37 outliers final: 18 residues processed: 163 average time/residue: 1.1687 time to fit residues: 204.3823 Evaluate side-chains 155 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 0.0670 chunk 43 optimal weight: 0.0170 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 chunk 106 optimal weight: 0.7980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN N 74 ASN N 82 GLN R 112 GLN R 263 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9431 Z= 0.155 Angle : 0.526 8.831 12787 Z= 0.276 Chirality : 0.039 0.148 1412 Planarity : 0.004 0.079 1623 Dihedral : 4.796 50.263 1269 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.95 % Allowed : 22.87 % Favored : 74.19 % 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: 0.01 (0.25), residues: 1133 helix: 1.46 (0.26), residues: 434 sheet: 0.32 (0.33), residues: 236 loop : -1.61 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.016 0.001 TYR R 145 ARG 0.013 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8034 (mt) cc_final: 0.7817 (mp) REVERT: A 283 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6944 (mtm110) REVERT: A 343 ASP cc_start: 0.6764 (m-30) cc_final: 0.6439 (m-30) REVERT: N 46 GLU cc_start: 0.7242 (mp0) cc_final: 0.6924 (mp0) REVERT: P 3 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: R 41 GLU cc_start: 0.8362 (pp20) cc_final: 0.8019 (pp20) REVERT: R 146 ILE cc_start: 0.8679 (mt) cc_final: 0.8434 (mp) REVERT: R 267 ARG cc_start: 0.6889 (tpt170) cc_final: 0.6283 (mpp80) REVERT: R 336 LYS cc_start: 0.7789 (mttp) cc_final: 0.7560 (mmtm) REVERT: R 348 ARG cc_start: 0.7499 (tpm-80) cc_final: 0.6345 (mtp180) REVERT: R 376 ARG cc_start: 0.7591 (ptp-170) cc_final: 0.6998 (mtt90) REVERT: R 383 LYS cc_start: 0.8559 (tttm) cc_final: 0.8321 (tttp) REVERT: R 387 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5757 (mt-10) REVERT: R 418 GLU cc_start: 0.7073 (tp30) cc_final: 0.6736 (tm-30) REVERT: B 134 ARG cc_start: 0.6593 (ptp-110) cc_final: 0.6342 (ptp-170) REVERT: B 186 ASP cc_start: 0.8010 (m-30) cc_final: 0.7631 (m-30) REVERT: B 221 THR cc_start: 0.8321 (t) cc_final: 0.8044 (m) REVERT: G 21 MET cc_start: 0.4032 (tmm) cc_final: 0.3737 (tpt) outliers start: 29 outliers final: 19 residues processed: 162 average time/residue: 1.1716 time to fit residues: 203.3279 Evaluate side-chains 151 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 382 ILE Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.0050 chunk 94 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN N 82 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9431 Z= 0.190 Angle : 0.543 7.672 12787 Z= 0.286 Chirality : 0.040 0.150 1412 Planarity : 0.005 0.079 1623 Dihedral : 4.781 49.287 1269 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.24 % Allowed : 24.09 % Favored : 73.68 % 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: 0.16 (0.25), residues: 1133 helix: 1.58 (0.26), residues: 431 sheet: 0.35 (0.33), residues: 236 loop : -1.47 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE B 235 TYR 0.017 0.001 TYR R 148 ARG 0.015 0.001 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8010 (mt) cc_final: 0.7805 (mp) REVERT: A 283 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6998 (mtm110) REVERT: A 343 ASP cc_start: 0.6820 (m-30) cc_final: 0.6503 (t0) REVERT: N 46 GLU cc_start: 0.7275 (mp0) cc_final: 0.6815 (mp0) REVERT: R 41 GLU cc_start: 0.8340 (pp20) cc_final: 0.7985 (pp20) REVERT: R 146 ILE cc_start: 0.8721 (mt) cc_final: 0.8461 (mp) REVERT: R 267 ARG cc_start: 0.6894 (tpt170) cc_final: 0.6290 (mpp80) REVERT: R 336 LYS cc_start: 0.7794 (mttp) cc_final: 0.7566 (mmtm) REVERT: R 348 ARG cc_start: 0.7500 (tpm-80) cc_final: 0.6341 (mtp180) REVERT: R 376 ARG cc_start: 0.7600 (ptp-170) cc_final: 0.7018 (mtt90) REVERT: R 383 LYS cc_start: 0.8574 (tttm) cc_final: 0.8335 (tttp) REVERT: R 387 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5730 (mt-10) REVERT: R 418 GLU cc_start: 0.7057 (tp30) cc_final: 0.6726 (tm-30) REVERT: B 186 ASP cc_start: 0.7993 (m-30) cc_final: 0.7464 (m-30) REVERT: G 21 MET cc_start: 0.4066 (tmm) cc_final: 0.3814 (tpt) outliers start: 22 outliers final: 17 residues processed: 152 average time/residue: 1.1640 time to fit residues: 189.6036 Evaluate side-chains 144 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 382 ILE Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN N 74 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.191688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145847 restraints weight = 10034.583| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.56 r_work: 0.3337 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9431 Z= 0.211 Angle : 0.557 7.652 12787 Z= 0.292 Chirality : 0.041 0.161 1412 Planarity : 0.005 0.079 1623 Dihedral : 4.829 49.462 1269 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.44 % Allowed : 24.29 % Favored : 73.27 % 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: 0.20 (0.25), residues: 1133 helix: 1.56 (0.26), residues: 431 sheet: 0.38 (0.33), residues: 236 loop : -1.40 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE B 235 TYR 0.018 0.001 TYR R 148 ARG 0.015 0.001 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3721.61 seconds wall clock time: 66 minutes 6.26 seconds (3966.26 seconds total)