Starting phenix.real_space_refine on Wed Feb 14 03:39:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/02_2024/6wi9_21683.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/02_2024/6wi9_21683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/02_2024/6wi9_21683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/02_2024/6wi9_21683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/02_2024/6wi9_21683.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/02_2024/6wi9_21683.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 53 5.16 5 C 5410 2.51 5 N 1526 2.21 5 O 1561 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 GLU 21": "OE1" <-> "OE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "R ARG 135": "NH1" <-> "NH2" Residue "R GLU 236": "OE1" <-> "OE2" Residue "R GLU 328": "OE1" <-> "OE2" Residue "R GLU 373": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1646 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2706 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 11, 'TRANS': 356} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 189 Time building chain proxies: 5.16, per 1000 atoms: 0.60 Number of scatterers: 8550 At special positions: 0 Unit cell: (78.26, 173.72, 97.18, 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 53 16.00 O 1561 8.00 N 1526 7.00 C 5410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 45 " - pdb=" SG CYS R 75 " distance=2.03 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " 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: 3.09 Conformation dependent library (CDL) restraints added in 1.8 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 40.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.503A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.702A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.720A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.761A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.685A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.962A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 36 removed outlier: 4.187A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 12 No H-bonds generated for 'chain 'G' and resid 10 through 12' Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.796A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.756A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'R' and resid 31 through 46 removed outlier: 4.010A pdb=" N ASP R 43 " --> pdb=" O TRP R 39 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN R 44 " --> pdb=" O GLU R 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS R 45 " --> pdb=" O GLU R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 50 Processing helix chain 'R' and resid 93 through 97 Processing helix chain 'R' and resid 131 through 165 removed outlier: 3.509A pdb=" N ARG R 135 " --> pdb=" O SER R 131 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS R 136 " --> pdb=" O ASN R 132 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL R 155 " --> pdb=" O SER R 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 200 removed outlier: 3.541A pdb=" N TYR R 176 " --> pdb=" O CYS R 172 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE R 177 " --> pdb=" O THR R 173 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N HIS R 180 " --> pdb=" O TYR R 176 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 193 " --> pdb=" O ALA R 189 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 246 removed outlier: 3.948A pdb=" N VAL R 220 " --> pdb=" O LYS R 216 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN R 229 " --> pdb=" O CYS R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 265 removed outlier: 3.603A pdb=" N GLY R 257 " --> pdb=" O LYS R 253 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 280 removed outlier: 4.095A pdb=" N ALA R 271 " --> pdb=" O ALA R 267 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 325 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 336 through 352 removed outlier: 4.617A pdb=" N ARG R 342 " --> pdb=" O LYS R 338 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU R 346 " --> pdb=" O ARG R 342 " (cutoff:3.500A) Proline residue: R 349 - end of helix Processing helix chain 'R' and resid 353 through 359 removed outlier: 3.977A pdb=" N PHE R 358 " --> pdb=" O TYR R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 368 removed outlier: 5.821A pdb=" N GLU R 367 " --> pdb=" O ASP R 364 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE R 368 " --> pdb=" O ALA R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 369 through 374 removed outlier: 3.569A pdb=" N GLU R 373 " --> pdb=" O GLN R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 378 No H-bonds generated for 'chain 'R' and resid 376 through 378' Processing helix chain 'R' and resid 379 through 390 Processing helix chain 'R' and resid 393 through 408 removed outlier: 3.514A pdb=" N GLU R 398 " --> pdb=" O GLU R 394 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL R 399 " --> pdb=" O VAL R 395 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS R 401 " --> pdb=" O LEU R 397 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS R 402 " --> pdb=" O GLU R 398 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS R 407 " --> pdb=" O TRP R 403 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 3.590A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 220 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.066A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.183A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.991A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.414A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.794A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.666A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.789A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.807A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 69 through 70 removed outlier: 3.677A pdb=" N MET R 69 " --> pdb=" O TRP R 76 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP R 76 " --> pdb=" O MET R 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 85 through 87 removed outlier: 4.269A pdb=" N LEU R 103 " --> pdb=" O VAL R 87 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1026 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: 2.80 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2851 1.35 - 1.46: 2108 1.46 - 1.58: 3684 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8716 Sorted by residual: bond pdb=" CA THR B 128 " pdb=" CB THR B 128 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.37e-02 5.33e+03 1.81e+00 bond pdb=" CA ILE R 246 " pdb=" CB ILE R 246 " ideal model delta sigma weight residual 1.533 1.545 -0.012 1.19e-02 7.06e+03 9.69e-01 bond pdb=" N GLY B 116 " pdb=" CA GLY B 116 " ideal model delta sigma weight residual 1.458 1.449 0.009 9.20e-03 1.18e+04 9.13e-01 bond pdb=" CA ILE N 51 " pdb=" CB ILE N 51 " ideal model delta sigma weight residual 1.550 1.541 0.009 1.03e-02 9.43e+03 7.69e-01 bond pdb=" C GLU R 67 " pdb=" N GLY R 68 " ideal model delta sigma weight residual 1.332 1.328 0.004 5.00e-03 4.00e+04 7.03e-01 ... (remaining 8711 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 171 107.14 - 113.85: 4839 113.85 - 120.55: 3384 120.55 - 127.26: 3315 127.26 - 133.97: 88 Bond angle restraints: 11797 Sorted by residual: angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 114.56 109.65 4.91 1.27e+00 6.20e-01 1.49e+01 angle pdb=" N ILE R 73 " pdb=" CA ILE R 73 " pdb=" C ILE R 73 " ideal model delta sigma weight residual 111.62 108.73 2.89 7.90e-01 1.60e+00 1.34e+01 angle pdb=" N ILE G 9 " pdb=" CA ILE G 9 " pdb=" C ILE G 9 " ideal model delta sigma weight residual 112.12 109.09 3.03 8.40e-01 1.42e+00 1.30e+01 angle pdb=" C GLU R 52 " pdb=" N GLN R 53 " pdb=" CA GLN R 53 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" N VAL N 64 " pdb=" CA VAL N 64 " pdb=" C VAL N 64 " ideal model delta sigma weight residual 113.20 110.06 3.14 9.60e-01 1.09e+00 1.07e+01 ... (remaining 11792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4768 17.83 - 35.67: 347 35.67 - 53.50: 39 53.50 - 71.34: 6 71.34 - 89.17: 15 Dihedral angle restraints: 5175 sinusoidal: 1970 harmonic: 3205 Sorted by residual: dihedral pdb=" CB CYS R 215 " pdb=" SG CYS R 215 " pdb=" SG CYS R 285 " pdb=" CB CYS R 285 " ideal model delta sinusoidal sigma weight residual 93.00 42.54 50.46 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CB CYS R 45 " pdb=" SG CYS R 45 " pdb=" SG CYS R 75 " pdb=" CB CYS R 75 " ideal model delta sinusoidal sigma weight residual 93.00 128.25 -35.25 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CB GLU R 373 " pdb=" CG GLU R 373 " pdb=" CD GLU R 373 " pdb=" OE1 GLU R 373 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 5172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 940 0.035 - 0.071: 282 0.071 - 0.106: 87 0.106 - 0.142: 12 0.142 - 0.177: 2 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CB ILE R 246 " pdb=" CA ILE R 246 " pdb=" CG1 ILE R 246 " pdb=" CG2 ILE R 246 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CB THR B 128 " pdb=" CA THR B 128 " pdb=" OG1 THR B 128 " pdb=" CG2 THR B 128 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA ILE R 288 " pdb=" N ILE R 288 " pdb=" C ILE R 288 " pdb=" CB ILE R 288 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 1320 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 236 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 321 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 300 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO R 301 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 301 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 301 " 0.017 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1049 2.75 - 3.29: 8547 3.29 - 3.83: 13270 3.83 - 4.36: 15713 4.36 - 4.90: 26736 Nonbonded interactions: 65315 Sorted by model distance: nonbonded pdb=" NH1 ARG B 42 " pdb=" O ILE B 43 " model vdw 2.214 2.520 nonbonded pdb=" O ASP B 76 " pdb=" OG SER B 98 " model vdw 2.236 2.440 nonbonded pdb=" O ARG R 339 " pdb=" OG SER R 343 " model vdw 2.312 2.440 nonbonded pdb=" OD1 ASN R 291 " pdb=" OG SER R 293 " model vdw 2.312 2.440 nonbonded pdb=" O GLY B 182 " pdb=" NZ LYS B 209 " model vdw 2.317 2.520 ... (remaining 65310 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 group one per residue 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: 0.710 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: 2.720 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.150 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.002 0.020 8716 Z= 0.110 Angle : 0.502 6.528 11797 Z= 0.312 Chirality : 0.038 0.177 1323 Planarity : 0.002 0.033 1516 Dihedral : 12.848 89.170 3086 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: -3.72 (0.21), residues: 1086 helix: -2.77 (0.18), residues: 377 sheet: -1.64 (0.32), residues: 208 loop : -2.50 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 234 HIS 0.001 0.000 HIS R 241 PHE 0.013 0.001 PHE A 315 TYR 0.004 0.001 TYR B 124 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 VAL cc_start: 0.8933 (t) cc_final: 0.8615 (t) REVERT: A 374 ARG cc_start: 0.7832 (mtt90) cc_final: 0.7522 (ttt180) REVERT: B 16 ASN cc_start: 0.9351 (m110) cc_final: 0.8821 (m110) REVERT: B 45 MET cc_start: 0.7078 (mmm) cc_final: 0.6780 (tpp) REVERT: B 78 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8541 (mmmt) REVERT: B 145 TYR cc_start: 0.8584 (p90) cc_final: 0.8363 (p90) REVERT: B 165 THR cc_start: 0.7995 (p) cc_final: 0.7711 (t) REVERT: B 188 MET cc_start: 0.7775 (tpt) cc_final: 0.7508 (mmm) REVERT: B 339 TRP cc_start: 0.8630 (m100) cc_final: 0.8350 (m100) REVERT: G 41 CYS cc_start: 0.8871 (m) cc_final: 0.8592 (m) REVERT: G 59 ASN cc_start: 0.7332 (t0) cc_final: 0.6484 (p0) REVERT: N 61 THR cc_start: 0.8397 (p) cc_final: 0.8140 (t) REVERT: N 83 MET cc_start: 0.8048 (pmm) cc_final: 0.7716 (pmm) REVERT: P 3 ASP cc_start: 0.8242 (t0) cc_final: 0.7914 (t0) REVERT: R 132 ASN cc_start: 0.8938 (p0) cc_final: 0.8731 (p0) REVERT: R 175 ASN cc_start: 0.9107 (m-40) cc_final: 0.8702 (m-40) REVERT: R 179 MET cc_start: 0.8074 (mmm) cc_final: 0.7814 (tpp) REVERT: R 230 TYR cc_start: 0.8606 (m-80) cc_final: 0.8047 (m-10) REVERT: R 256 GLN cc_start: 0.7622 (mt0) cc_final: 0.6522 (tm-30) REVERT: R 261 PHE cc_start: 0.9038 (t80) cc_final: 0.8828 (t80) REVERT: R 282 ASP cc_start: 0.7871 (t0) cc_final: 0.7609 (t0) REVERT: R 321 MET cc_start: 0.8108 (mtt) cc_final: 0.7812 (mmm) REVERT: R 354 HIS cc_start: 0.9050 (p-80) cc_final: 0.8655 (p-80) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2357 time to fit residues: 99.1317 Evaluate side-chains 211 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.0270 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 97 optimal weight: 0.8980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 218 ASN B 17 GLN B 91 HIS B 220 GLN N 3 GLN R 180 HIS R 223 GLN R 229 ASN ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8716 Z= 0.176 Angle : 0.561 6.480 11797 Z= 0.301 Chirality : 0.042 0.189 1323 Planarity : 0.004 0.037 1516 Dihedral : 3.733 16.222 1203 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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: -1.94 (0.24), residues: 1086 helix: -0.45 (0.25), residues: 375 sheet: -1.07 (0.34), residues: 201 loop : -2.00 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 295 HIS 0.005 0.001 HIS R 241 PHE 0.022 0.002 PHE N 68 TYR 0.017 0.001 TYR R 138 ARG 0.006 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9297 (mp) cc_final: 0.9013 (mm) REVERT: A 221 MET cc_start: 0.8380 (tpt) cc_final: 0.8122 (tpp) REVERT: A 222 PHE cc_start: 0.7974 (m-80) cc_final: 0.7709 (m-80) REVERT: A 318 TYR cc_start: 0.7873 (t80) cc_final: 0.7217 (t80) REVERT: A 374 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7448 (ttt180) REVERT: B 16 ASN cc_start: 0.9068 (m110) cc_final: 0.8645 (m110) REVERT: B 78 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8399 (mmmt) REVERT: B 188 MET cc_start: 0.8140 (tpt) cc_final: 0.7765 (mmm) REVERT: B 209 LYS cc_start: 0.8942 (mttt) cc_final: 0.8691 (mmmm) REVERT: B 217 MET cc_start: 0.8686 (ppp) cc_final: 0.8206 (ppp) REVERT: B 220 GLN cc_start: 0.8544 (tt0) cc_final: 0.8292 (tt0) REVERT: B 225 HIS cc_start: 0.7290 (m-70) cc_final: 0.7079 (m-70) REVERT: G 21 MET cc_start: 0.7942 (mmm) cc_final: 0.7171 (mmm) REVERT: G 59 ASN cc_start: 0.7222 (t0) cc_final: 0.6122 (p0) REVERT: N 68 PHE cc_start: 0.8119 (m-10) cc_final: 0.7776 (m-10) REVERT: R 175 ASN cc_start: 0.9083 (m-40) cc_final: 0.8704 (m-40) REVERT: R 179 MET cc_start: 0.8009 (mmm) cc_final: 0.7700 (tpp) REVERT: R 230 TYR cc_start: 0.8681 (m-80) cc_final: 0.8461 (m-10) REVERT: R 251 GLU cc_start: 0.7547 (pm20) cc_final: 0.7252 (pm20) REVERT: R 282 ASP cc_start: 0.7833 (t0) cc_final: 0.6915 (t0) REVERT: R 321 MET cc_start: 0.8110 (mtt) cc_final: 0.7824 (mmm) REVERT: R 342 ARG cc_start: 0.8384 (mtm180) cc_final: 0.7891 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2130 time to fit residues: 76.5093 Evaluate side-chains 207 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 91 HIS R 229 ASN R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8716 Z= 0.160 Angle : 0.537 6.300 11797 Z= 0.285 Chirality : 0.041 0.135 1323 Planarity : 0.004 0.037 1516 Dihedral : 3.794 14.933 1203 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % 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: -1.38 (0.25), residues: 1086 helix: 0.14 (0.26), residues: 382 sheet: -0.83 (0.34), residues: 201 loop : -1.77 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 286 HIS 0.005 0.001 HIS B 225 PHE 0.034 0.002 PHE A 340 TYR 0.017 0.001 TYR R 138 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7827 (mtt90) cc_final: 0.7336 (mtt180) REVERT: B 78 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8365 (mmmt) REVERT: B 188 MET cc_start: 0.8088 (tpt) cc_final: 0.7780 (mmm) REVERT: B 209 LYS cc_start: 0.8818 (mttt) cc_final: 0.8563 (mmmm) REVERT: B 217 MET cc_start: 0.8622 (ppp) cc_final: 0.8281 (ppp) REVERT: B 220 GLN cc_start: 0.8435 (tt0) cc_final: 0.7964 (tt0) REVERT: B 225 HIS cc_start: 0.7146 (m-70) cc_final: 0.6908 (m-70) REVERT: B 308 LEU cc_start: 0.8947 (mt) cc_final: 0.8688 (mp) REVERT: G 14 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8163 (mtmm) REVERT: G 21 MET cc_start: 0.7965 (mmm) cc_final: 0.7002 (mmm) REVERT: G 41 CYS cc_start: 0.8768 (m) cc_final: 0.8430 (m) REVERT: G 59 ASN cc_start: 0.7221 (t0) cc_final: 0.6150 (p0) REVERT: N 64 VAL cc_start: 0.8017 (m) cc_final: 0.7536 (m) REVERT: N 73 ASP cc_start: 0.7822 (t70) cc_final: 0.7324 (t70) REVERT: N 76 LYS cc_start: 0.8943 (mtmm) cc_final: 0.8301 (mtmm) REVERT: R 175 ASN cc_start: 0.9063 (m-40) cc_final: 0.8642 (m-40) REVERT: R 179 MET cc_start: 0.7901 (mmm) cc_final: 0.7684 (tpp) REVERT: R 321 MET cc_start: 0.8080 (mtt) cc_final: 0.7777 (mmm) REVERT: R 355 TYR cc_start: 0.8629 (m-80) cc_final: 0.8074 (m-80) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2033 time to fit residues: 70.4014 Evaluate side-chains 207 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 17 GLN B 175 GLN R 229 ASN R 392 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8716 Z= 0.184 Angle : 0.539 6.450 11797 Z= 0.286 Chirality : 0.041 0.225 1323 Planarity : 0.004 0.038 1516 Dihedral : 3.909 16.232 1203 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 1086 helix: 0.46 (0.27), residues: 383 sheet: -0.56 (0.35), residues: 205 loop : -1.58 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 295 HIS 0.006 0.001 HIS R 241 PHE 0.027 0.002 PHE A 340 TYR 0.023 0.002 TYR R 150 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7860 (mtt90) cc_final: 0.7346 (mtt180) REVERT: B 78 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8328 (mmmt) REVERT: B 209 LYS cc_start: 0.8931 (mttt) cc_final: 0.8543 (mmmm) REVERT: B 217 MET cc_start: 0.8626 (ppp) cc_final: 0.8209 (ppp) REVERT: B 220 GLN cc_start: 0.8152 (tt0) cc_final: 0.7932 (tt0) REVERT: G 41 CYS cc_start: 0.8707 (m) cc_final: 0.8289 (m) REVERT: G 59 ASN cc_start: 0.7358 (t0) cc_final: 0.7078 (t0) REVERT: N 64 VAL cc_start: 0.8033 (m) cc_final: 0.7722 (m) REVERT: N 73 ASP cc_start: 0.7545 (t70) cc_final: 0.7094 (t0) REVERT: N 76 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8342 (mtmm) REVERT: N 84 ASN cc_start: 0.8965 (p0) cc_final: 0.8722 (p0) REVERT: R 147 THR cc_start: 0.8884 (m) cc_final: 0.8629 (m) REVERT: R 175 ASN cc_start: 0.9050 (m-40) cc_final: 0.8609 (m-40) REVERT: R 179 MET cc_start: 0.7915 (mmm) cc_final: 0.7712 (tpp) REVERT: R 321 MET cc_start: 0.8106 (mtt) cc_final: 0.7786 (mmm) REVERT: R 355 TYR cc_start: 0.8687 (m-80) cc_final: 0.8381 (m-80) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.2055 time to fit residues: 71.2225 Evaluate side-chains 197 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 175 GLN G 24 ASN N 53 GLN R 229 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8716 Z= 0.373 Angle : 0.683 6.144 11797 Z= 0.363 Chirality : 0.045 0.170 1323 Planarity : 0.005 0.044 1516 Dihedral : 4.640 18.509 1203 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.23 % Allowed : 3.79 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.26), residues: 1086 helix: 0.19 (0.26), residues: 377 sheet: -0.73 (0.35), residues: 224 loop : -1.59 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 281 HIS 0.011 0.002 HIS R 241 PHE 0.020 0.002 PHE A 340 TYR 0.020 0.002 TYR R 138 ARG 0.009 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 233 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7505 (mtt180) REVERT: B 6 GLN cc_start: 0.9277 (tp40) cc_final: 0.8975 (tp-100) REVERT: B 209 LYS cc_start: 0.8974 (mttt) cc_final: 0.8547 (mmmm) REVERT: B 220 GLN cc_start: 0.8188 (tt0) cc_final: 0.7883 (tt0) REVERT: G 41 CYS cc_start: 0.8760 (m) cc_final: 0.8463 (m) REVERT: G 59 ASN cc_start: 0.7600 (t0) cc_final: 0.6831 (t0) REVERT: N 64 VAL cc_start: 0.8103 (m) cc_final: 0.7773 (m) REVERT: N 73 ASP cc_start: 0.7609 (t70) cc_final: 0.7014 (t0) REVERT: N 76 LYS cc_start: 0.9033 (mtmm) cc_final: 0.8350 (mtmm) REVERT: N 84 ASN cc_start: 0.8787 (p0) cc_final: 0.8493 (p0) REVERT: N 117 TYR cc_start: 0.8552 (m-80) cc_final: 0.8304 (m-80) REVERT: R 147 THR cc_start: 0.8902 (m) cc_final: 0.8685 (m) REVERT: R 156 MET cc_start: 0.8023 (tpt) cc_final: 0.7798 (tpt) REVERT: R 175 ASN cc_start: 0.9161 (m-40) cc_final: 0.8800 (m-40) REVERT: R 179 MET cc_start: 0.8112 (mmm) cc_final: 0.7862 (mmm) REVERT: R 221 LEU cc_start: 0.9396 (tp) cc_final: 0.9128 (pp) REVERT: R 321 MET cc_start: 0.8246 (mtt) cc_final: 0.7927 (mmm) outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 0.2102 time to fit residues: 67.4916 Evaluate side-chains 188 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 175 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8716 Z= 0.172 Angle : 0.566 6.684 11797 Z= 0.299 Chirality : 0.041 0.141 1323 Planarity : 0.003 0.044 1516 Dihedral : 4.342 17.504 1203 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.23 % Allowed : 2.07 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.26), residues: 1086 helix: 0.57 (0.27), residues: 377 sheet: -0.55 (0.36), residues: 207 loop : -1.52 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.006 0.001 HIS B 54 PHE 0.021 0.001 PHE A 340 TYR 0.024 0.002 TYR G 40 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.9363 (m110) cc_final: 0.9081 (m110) REVERT: B 78 LYS cc_start: 0.8323 (mmtm) cc_final: 0.7969 (mmtm) REVERT: B 209 LYS cc_start: 0.8825 (mttt) cc_final: 0.8429 (mttt) REVERT: B 217 MET cc_start: 0.8640 (ppp) cc_final: 0.7919 (ppp) REVERT: B 222 PHE cc_start: 0.8429 (m-80) cc_final: 0.8093 (m-10) REVERT: B 318 LEU cc_start: 0.8819 (mt) cc_final: 0.8375 (mp) REVERT: G 59 ASN cc_start: 0.7413 (t0) cc_final: 0.6742 (t0) REVERT: N 68 PHE cc_start: 0.8399 (m-10) cc_final: 0.7816 (m-10) REVERT: N 117 TYR cc_start: 0.8357 (m-80) cc_final: 0.8059 (m-80) REVERT: R 147 THR cc_start: 0.8822 (m) cc_final: 0.8601 (m) REVERT: R 175 ASN cc_start: 0.8979 (m-40) cc_final: 0.8650 (m-40) REVERT: R 179 MET cc_start: 0.7908 (mmm) cc_final: 0.7705 (tpp) REVERT: R 221 LEU cc_start: 0.9353 (tp) cc_final: 0.9084 (pp) REVERT: R 321 MET cc_start: 0.8134 (mtt) cc_final: 0.7766 (mmm) REVERT: R 372 PHE cc_start: 0.6717 (m-80) cc_final: 0.5752 (m-80) outliers start: 2 outliers final: 0 residues processed: 250 average time/residue: 0.1999 time to fit residues: 68.5184 Evaluate side-chains 190 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 0.3980 chunk 103 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 175 GLN N 82 GLN R 229 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8716 Z= 0.187 Angle : 0.579 7.416 11797 Z= 0.305 Chirality : 0.042 0.257 1323 Planarity : 0.004 0.047 1516 Dihedral : 4.314 16.693 1203 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.23 % Allowed : 1.15 % Favored : 98.62 % 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: -0.71 (0.26), residues: 1086 helix: 0.68 (0.27), residues: 383 sheet: -0.49 (0.35), residues: 215 loop : -1.37 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 286 HIS 0.006 0.001 HIS R 241 PHE 0.031 0.002 PHE N 68 TYR 0.014 0.001 TYR A 318 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 237 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7527 (mtt180) REVERT: B 209 LYS cc_start: 0.8898 (mttt) cc_final: 0.8436 (mttt) REVERT: B 217 MET cc_start: 0.8639 (ppp) cc_final: 0.7977 (ppp) REVERT: B 318 LEU cc_start: 0.8849 (mt) cc_final: 0.8606 (mt) REVERT: G 59 ASN cc_start: 0.7409 (t0) cc_final: 0.6741 (t0) REVERT: N 80 TYR cc_start: 0.6962 (m-10) cc_final: 0.6285 (m-80) REVERT: R 147 THR cc_start: 0.8814 (m) cc_final: 0.8596 (m) REVERT: R 175 ASN cc_start: 0.8919 (m-40) cc_final: 0.8666 (m-40) REVERT: R 221 LEU cc_start: 0.9344 (tp) cc_final: 0.9083 (pp) REVERT: R 251 GLU cc_start: 0.7480 (pm20) cc_final: 0.7041 (pp20) REVERT: R 313 PHE cc_start: 0.8846 (t80) cc_final: 0.8605 (t80) REVERT: R 321 MET cc_start: 0.8143 (mtt) cc_final: 0.7771 (mmm) REVERT: R 387 LEU cc_start: 0.8325 (tt) cc_final: 0.8057 (tt) outliers start: 2 outliers final: 1 residues processed: 239 average time/residue: 0.1864 time to fit residues: 61.8388 Evaluate side-chains 180 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8716 Z= 0.186 Angle : 0.591 7.925 11797 Z= 0.310 Chirality : 0.042 0.227 1323 Planarity : 0.004 0.052 1516 Dihedral : 4.322 16.513 1203 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -0.71 (0.26), residues: 1086 helix: 0.61 (0.27), residues: 386 sheet: -0.34 (0.36), residues: 208 loop : -1.38 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 281 HIS 0.005 0.001 HIS R 241 PHE 0.030 0.001 PHE N 68 TYR 0.017 0.002 TYR A 360 ARG 0.004 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7547 (mtt180) REVERT: B 217 MET cc_start: 0.8629 (ppp) cc_final: 0.7932 (ppp) REVERT: B 318 LEU cc_start: 0.8826 (mt) cc_final: 0.8434 (mp) REVERT: G 59 ASN cc_start: 0.7386 (t0) cc_final: 0.6700 (t0) REVERT: R 221 LEU cc_start: 0.9335 (tp) cc_final: 0.9066 (pp) REVERT: R 251 GLU cc_start: 0.7492 (pm20) cc_final: 0.6937 (pp20) REVERT: R 313 PHE cc_start: 0.8852 (t80) cc_final: 0.8621 (t80) REVERT: R 321 MET cc_start: 0.8121 (mtt) cc_final: 0.7758 (mmm) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1913 time to fit residues: 63.7092 Evaluate side-chains 185 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 101 optimal weight: 0.0370 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 225 HIS N 53 GLN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8716 Z= 0.167 Angle : 0.604 10.275 11797 Z= 0.312 Chirality : 0.042 0.217 1323 Planarity : 0.004 0.055 1516 Dihedral : 4.311 17.574 1203 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.11 % Allowed : 1.15 % Favored : 98.74 % 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: -0.66 (0.26), residues: 1086 helix: 0.64 (0.27), residues: 386 sheet: -0.29 (0.36), residues: 208 loop : -1.35 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 281 HIS 0.007 0.001 HIS B 225 PHE 0.033 0.002 PHE N 68 TYR 0.027 0.002 TYR A 318 ARG 0.006 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.9345 (m110) cc_final: 0.9128 (m110) REVERT: B 78 LYS cc_start: 0.8669 (mmpt) cc_final: 0.8333 (mmmt) REVERT: B 209 LYS cc_start: 0.8867 (mttt) cc_final: 0.8386 (mttt) REVERT: B 217 MET cc_start: 0.8696 (ppp) cc_final: 0.8234 (ppp) REVERT: B 318 LEU cc_start: 0.8858 (mt) cc_final: 0.8418 (mp) REVERT: G 14 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8047 (mtmm) REVERT: G 59 ASN cc_start: 0.7361 (t0) cc_final: 0.6966 (t0) REVERT: N 76 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8427 (mtmm) REVERT: R 147 THR cc_start: 0.8729 (m) cc_final: 0.8480 (m) REVERT: R 221 LEU cc_start: 0.9311 (tp) cc_final: 0.9070 (pp) REVERT: R 321 MET cc_start: 0.8099 (mtt) cc_final: 0.7722 (mmm) REVERT: R 346 LEU cc_start: 0.8009 (tp) cc_final: 0.7717 (tp) REVERT: R 406 TRP cc_start: 0.7641 (t60) cc_final: 0.6289 (m100) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.2018 time to fit residues: 67.2465 Evaluate side-chains 191 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 65 optimal weight: 0.0000 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN R 392 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8716 Z= 0.163 Angle : 0.611 10.523 11797 Z= 0.309 Chirality : 0.042 0.240 1323 Planarity : 0.004 0.057 1516 Dihedral : 4.144 18.523 1203 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.11 % Allowed : 0.46 % Favored : 99.43 % 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: -0.58 (0.26), residues: 1086 helix: 0.74 (0.27), residues: 392 sheet: -0.17 (0.36), residues: 206 loop : -1.40 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 281 HIS 0.004 0.001 HIS G 44 PHE 0.030 0.001 PHE N 68 TYR 0.027 0.001 TYR A 318 ARG 0.005 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.9240 (mm) cc_final: 0.9037 (mm) REVERT: B 78 LYS cc_start: 0.8581 (mmpt) cc_final: 0.8313 (mmmt) REVERT: B 209 LYS cc_start: 0.8774 (mttt) cc_final: 0.8282 (mttt) REVERT: B 217 MET cc_start: 0.8636 (ppp) cc_final: 0.8193 (ppp) REVERT: B 318 LEU cc_start: 0.8802 (mt) cc_final: 0.8382 (mp) REVERT: G 59 ASN cc_start: 0.7363 (t0) cc_final: 0.7047 (t0) REVERT: N 81 LEU cc_start: 0.7459 (tt) cc_final: 0.5998 (tt) REVERT: N 83 MET cc_start: 0.6460 (mmp) cc_final: 0.6001 (tpt) REVERT: R 150 TYR cc_start: 0.7653 (m-10) cc_final: 0.7401 (m-80) REVERT: R 175 ASN cc_start: 0.8749 (m-40) cc_final: 0.8204 (m-40) REVERT: R 221 LEU cc_start: 0.9301 (tp) cc_final: 0.9081 (pp) REVERT: R 321 MET cc_start: 0.8088 (mtt) cc_final: 0.7688 (mmm) REVERT: R 355 TYR cc_start: 0.8374 (m-80) cc_final: 0.8091 (m-10) REVERT: R 406 TRP cc_start: 0.7615 (t60) cc_final: 0.6264 (m100) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.1802 time to fit residues: 60.9830 Evaluate side-chains 192 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 50.0000 chunk 12 optimal weight: 0.0770 chunk 23 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 10 optimal weight: 0.0470 chunk 15 optimal weight: 3.9990 chunk 74 optimal weight: 50.0000 chunk 4 optimal weight: 5.9990 overall best weight: 2.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 175 GLN ** R 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN R 289 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.106885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084137 restraints weight = 23792.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086653 restraints weight = 14099.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088366 restraints weight = 9793.699| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8716 Z= 0.225 Angle : 0.643 13.656 11797 Z= 0.328 Chirality : 0.043 0.277 1323 Planarity : 0.004 0.045 1516 Dihedral : 4.327 19.532 1203 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.11 % Allowed : 0.69 % Favored : 99.20 % 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: -0.69 (0.26), residues: 1086 helix: 0.72 (0.27), residues: 392 sheet: -0.38 (0.35), residues: 211 loop : -1.47 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 36 HIS 0.008 0.001 HIS R 241 PHE 0.018 0.001 PHE A 315 TYR 0.027 0.002 TYR A 318 ARG 0.008 0.000 ARG N 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.05 seconds wall clock time: 41 minutes 17.68 seconds (2477.68 seconds total)