Starting phenix.real_space_refine (version: dev) on Sat Feb 18 20:29:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d77_32838/02_2023/7d77_32838.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d77_32838/02_2023/7d77_32838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d77_32838/02_2023/7d77_32838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d77_32838/02_2023/7d77_32838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d77_32838/02_2023/7d77_32838.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d77_32838/02_2023/7d77_32838.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 Process input model Symmetric amino acids flipped Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "R PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 303": "OE1" <-> "OE2" Residue "R ASP 304": "OD1" <-> "OD2" Residue "R ARG 369": "NH1" <-> "NH2" Residue "R TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 414": "NH1" <-> "NH2" Residue "R ARG 462": "NH1" <-> "NH2" Residue "R ARG 469": "NH1" <-> "NH2" Residue "R PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 125": "OD1" <-> "OD2" Residue "S ARG 206": "NH1" <-> "NH2" Residue "S GLU 208": "OE1" <-> "OE2" Residue "S ASP 211": "OD1" <-> "OD2" Residue "S TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8785 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1711 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 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: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2097 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 4, 'TRANS': 260} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 154 Unusual residues: {'CLR': 2, 'HCY': 1, 'PLM': 2, 'Y01': 1} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Time building chain proxies: 5.38, per 1000 atoms: 0.61 Number of scatterers: 8785 At special positions: 0 Unit cell: (107, 126, 113, 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 56 16.00 O 1618 8.00 N 1466 7.00 C 5645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 338 " - pdb=" SG CYS R 420 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.4 seconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 15 sheets defined 33.6% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.950A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.622A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.908A pdb=" N ILE A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.765A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'R' and resid 264 through 297 removed outlier: 4.068A pdb=" N PHE R 282 " --> pdb=" O VAL R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 303 removed outlier: 3.850A pdb=" N GLU R 303 " --> pdb=" O PHE R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 329 Processing helix chain 'R' and resid 334 through 368 removed outlier: 3.816A pdb=" N CYS R 338 " --> pdb=" O SER R 334 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA R 340 " --> pdb=" O ALA R 336 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA R 360 " --> pdb=" O MET R 356 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 400 Proline residue: R 390 - end of helix removed outlier: 3.723A pdb=" N ALA R 400 " --> pdb=" O GLY R 396 " (cutoff:3.500A) Processing helix chain 'R' and resid 428 through 435 removed outlier: 4.323A pdb=" N TYR R 432 " --> pdb=" O MET R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 461 Processing helix chain 'R' and resid 471 through 495 removed outlier: 3.673A pdb=" N LYS R 475 " --> pdb=" O LYS R 471 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU R 477 " --> pdb=" O ARG R 473 " (cutoff:3.500A) Processing helix chain 'R' and resid 502 through 525 removed outlier: 3.549A pdb=" N PHE R 506 " --> pdb=" O THR R 502 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE R 517 " --> pdb=" O GLN R 513 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.503A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.503A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.449A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.521A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.884A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.835A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.709A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.801A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.451A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 403 through 409 removed outlier: 3.577A pdb=" N LEU R 417 " --> pdb=" O ILE R 408 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.627A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.147A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.147A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.440A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 147 405 hydrogen bonds defined for protein. 1152 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: 2.83 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1407 1.32 - 1.45: 2518 1.45 - 1.58: 4964 1.58 - 1.70: 8 1.70 - 1.83: 80 Bond restraints: 8977 Sorted by residual: bond pdb=" CAS Y01 R 601 " pdb=" CAU Y01 R 601 " ideal model delta sigma weight residual 1.530 1.304 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" CBE Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 1.550 1.375 0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" CAS Y01 R 601 " pdb=" CBF Y01 R 601 " ideal model delta sigma weight residual 1.533 1.363 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" CBF Y01 R 601 " pdb=" CBH Y01 R 601 " ideal model delta sigma weight residual 1.550 1.689 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" CAP Y01 R 601 " pdb=" CAQ Y01 R 601 " ideal model delta sigma weight residual 1.541 1.654 -0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 8972 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.00: 147 106.00 - 113.02: 4929 113.02 - 120.04: 3117 120.04 - 127.07: 3877 127.07 - 134.09: 93 Bond angle restraints: 12163 Sorted by residual: angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 132.52 -10.98 1.91e+00 2.74e-01 3.30e+01 angle pdb=" N ARG R 411 " pdb=" CA ARG R 411 " pdb=" C ARG R 411 " ideal model delta sigma weight residual 112.54 105.87 6.67 1.22e+00 6.72e-01 2.99e+01 angle pdb=" CBD Y01 R 601 " pdb=" CBG Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 115.11 105.59 9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N ASN A 295 " pdb=" CA ASN A 295 " pdb=" C ASN A 295 " ideal model delta sigma weight residual 108.52 113.97 -5.45 1.74e+00 3.30e-01 9.82e+00 angle pdb=" CBB Y01 R 601 " pdb=" CBE Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 119.27 110.15 9.12 3.00e+00 1.11e-01 9.24e+00 ... (remaining 12158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 4908 21.33 - 42.66: 306 42.66 - 63.99: 28 63.99 - 85.32: 7 85.32 - 106.65: 2 Dihedral angle restraints: 5251 sinusoidal: 2072 harmonic: 3179 Sorted by residual: dihedral pdb=" CB CYS R 338 " pdb=" SG CYS R 338 " pdb=" SG CYS R 420 " pdb=" CB CYS R 420 " ideal model delta sinusoidal sigma weight residual -86.00 -33.18 -52.82 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA GLN A 52 " pdb=" C GLN A 52 " pdb=" N MET A 53 " pdb=" CA MET A 53 " ideal model delta harmonic sigma weight residual -180.00 -157.51 -22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR A 188 " pdb=" C THR A 188 " pdb=" N HIS A 189 " pdb=" CA HIS A 189 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 5248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1314 0.109 - 0.217: 53 0.217 - 0.326: 7 0.326 - 0.434: 2 0.434 - 0.543: 1 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CBG Y01 R 601 " pdb=" CAQ Y01 R 601 " pdb=" CBD Y01 R 601 " pdb=" CBI Y01 R 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" C14 CLR R 606 " pdb=" C13 CLR R 606 " pdb=" C15 CLR R 606 " pdb=" C8 CLR R 606 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 1374 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 HCY R 604 " -0.022 2.00e-02 2.50e+03 7.73e-02 7.46e+01 pdb=" C3 HCY R 604 " 0.095 2.00e-02 2.50e+03 pdb=" C4 HCY R 604 " -0.121 2.00e-02 2.50e+03 pdb=" C5 HCY R 604 " -0.023 2.00e-02 2.50e+03 pdb=" C6 HCY R 604 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 235 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C PHE B 235 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE B 235 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO B 236 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 410 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C ASP R 410 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP R 410 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG R 411 " 0.012 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 154 2.67 - 3.22: 8050 3.22 - 3.78: 12843 3.78 - 4.34: 18190 4.34 - 4.90: 31345 Nonbonded interactions: 70582 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.107 2.440 nonbonded pdb=" NZ LYS A 210 " pdb=" OD2 ASP B 228 " model vdw 2.132 2.520 nonbonded pdb=" O THR R 397 " pdb=" OG SER R 402 " model vdw 2.135 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.136 2.440 nonbonded pdb=" OG SER S 149 " pdb=" O LYS S 151 " model vdw 2.157 2.440 ... (remaining 70577 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5645 2.51 5 N 1466 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 2.370 Check model and map are aligned: 0.140 Process input model: 25.550 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0106 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 : 0.008 0.226 8977 Z= 0.560 Angle : 0.778 10.977 12163 Z= 0.404 Chirality : 0.056 0.543 1377 Planarity : 0.004 0.077 1511 Dihedral : 13.513 106.650 3205 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.22), residues: 1091 helix: -0.32 (0.25), residues: 352 sheet: -1.90 (0.28), residues: 274 loop : -2.64 (0.24), residues: 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.893 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 1.0750 time to fit residues: 91.1652 Evaluate side-chains 44 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0020 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.0070 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 362 HIS ** R 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0276 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8977 Z= 0.145 Angle : 0.536 7.375 12163 Z= 0.277 Chirality : 0.041 0.147 1377 Planarity : 0.003 0.036 1511 Dihedral : 6.178 52.504 1276 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.08 (0.24), residues: 1091 helix: 1.30 (0.27), residues: 362 sheet: -1.37 (0.28), residues: 274 loop : -1.96 (0.26), residues: 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.896 Fit side-chains outliers start: 15 outliers final: 2 residues processed: 57 average time/residue: 1.1419 time to fit residues: 70.8399 Evaluate side-chains 44 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.3173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.0270 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 30.0000 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 156 GLN ** R 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0742 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8977 Z= 0.183 Angle : 0.597 8.568 12163 Z= 0.305 Chirality : 0.042 0.146 1377 Planarity : 0.004 0.049 1511 Dihedral : 6.058 57.635 1276 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.60 (0.25), residues: 1091 helix: 1.48 (0.28), residues: 367 sheet: -0.98 (0.28), residues: 278 loop : -1.59 (0.27), residues: 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 1.059 Fit side-chains outliers start: 17 outliers final: 5 residues processed: 59 average time/residue: 1.0014 time to fit residues: 65.1429 Evaluate side-chains 42 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.1376 time to fit residues: 1.6242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 0.0470 chunk 104 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN R 472 ASN R 510 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0968 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8977 Z= 0.193 Angle : 0.606 9.802 12163 Z= 0.305 Chirality : 0.041 0.173 1377 Planarity : 0.004 0.072 1511 Dihedral : 6.388 49.432 1276 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.37 (0.25), residues: 1091 helix: 1.57 (0.28), residues: 359 sheet: -0.58 (0.29), residues: 272 loop : -1.49 (0.28), residues: 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 39 time to evaluate : 1.083 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 55 average time/residue: 1.0070 time to fit residues: 61.1873 Evaluate side-chains 47 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 35 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.6788 time to fit residues: 2.8656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.2980 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 40.0000 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0903 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8977 Z= 0.129 Angle : 0.484 7.336 12163 Z= 0.251 Chirality : 0.039 0.153 1377 Planarity : 0.003 0.039 1511 Dihedral : 5.726 52.451 1276 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.02 (0.26), residues: 1091 helix: 1.89 (0.28), residues: 363 sheet: -0.46 (0.30), residues: 270 loop : -1.21 (0.28), residues: 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 39 time to evaluate : 0.885 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 56 average time/residue: 0.8513 time to fit residues: 53.4249 Evaluate side-chains 48 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 34 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 2 average time/residue: 0.6176 time to fit residues: 2.7372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 86 optimal weight: 0.0270 chunk 48 optimal weight: 10.0000 chunk 8 optimal weight: 0.0770 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.0670 overall best weight: 0.8136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0923 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 8977 Z= 0.124 Angle : 0.497 8.462 12163 Z= 0.254 Chirality : 0.039 0.153 1377 Planarity : 0.003 0.038 1511 Dihedral : 5.664 52.777 1276 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.10 (0.26), residues: 1091 helix: 1.94 (0.28), residues: 362 sheet: -0.42 (0.30), residues: 270 loop : -1.14 (0.28), residues: 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 38 time to evaluate : 0.901 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 55 average time/residue: 0.8906 time to fit residues: 54.7982 Evaluate side-chains 48 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.6532 time to fit residues: 3.0199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 chunk 58 optimal weight: 0.0370 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1135 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8977 Z= 0.198 Angle : 0.609 9.970 12163 Z= 0.311 Chirality : 0.042 0.225 1377 Planarity : 0.004 0.056 1511 Dihedral : 6.959 55.127 1276 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.13 (0.25), residues: 1091 helix: 1.63 (0.28), residues: 357 sheet: -0.19 (0.31), residues: 253 loop : -1.36 (0.27), residues: 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 0.795 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 52 average time/residue: 0.8922 time to fit residues: 51.8039 Evaluate side-chains 50 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 36 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.5980 time to fit residues: 2.6931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 70 optimal weight: 0.0870 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1190 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 8977 Z= 0.197 Angle : 0.616 11.250 12163 Z= 0.311 Chirality : 0.042 0.180 1377 Planarity : 0.004 0.047 1511 Dihedral : 6.950 54.111 1276 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.24 (0.25), residues: 1091 helix: 1.39 (0.28), residues: 360 sheet: -0.12 (0.31), residues: 262 loop : -1.43 (0.28), residues: 469 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 36 time to evaluate : 1.113 Fit side-chains outliers start: 21 outliers final: 18 residues processed: 56 average time/residue: 0.8929 time to fit residues: 55.9263 Evaluate side-chains 52 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 34 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 1.1258 time to fit residues: 2.6176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 40.0000 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 155 ASN R 436 HIS S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1213 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8977 Z= 0.175 Angle : 0.580 9.509 12163 Z= 0.294 Chirality : 0.042 0.191 1377 Planarity : 0.004 0.039 1511 Dihedral : 6.836 50.485 1276 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.22 (0.25), residues: 1091 helix: 1.38 (0.28), residues: 361 sheet: -0.04 (0.31), residues: 261 loop : -1.43 (0.28), residues: 469 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 37 time to evaluate : 0.918 Fit side-chains outliers start: 19 outliers final: 19 residues processed: 55 average time/residue: 0.8023 time to fit residues: 49.8444 Evaluate side-chains 53 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 34 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 1.3650 time to fit residues: 3.0053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 48 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 68 optimal weight: 0.0980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 436 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1100 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8977 Z= 0.126 Angle : 0.512 10.476 12163 Z= 0.260 Chirality : 0.040 0.179 1377 Planarity : 0.003 0.044 1511 Dihedral : 6.190 51.194 1276 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.14 (0.26), residues: 1091 helix: 1.77 (0.28), residues: 361 sheet: 0.19 (0.32), residues: 252 loop : -1.29 (0.28), residues: 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 33 time to evaluate : 0.921 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 18 residues processed: 51 average time/residue: 0.8710 time to fit residues: 49.9444 Evaluate side-chains 50 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 32 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 1.0713 time to fit residues: 2.5282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 0.0870 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 85 optimal weight: 40.0000 chunk 35 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 overall best weight: 3.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 436 HIS ** R 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5594 r_free = 0.5594 target = 0.387983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5513 r_free = 0.5513 target = 0.376078 restraints weight = 13175.426| |-----------------------------------------------------------------------------| r_work (start): 0.5524 rms_B_bonded: 1.73 r_work: 0.5482 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.5415 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.5415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1772 moved from start: 0.7594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 8977 Z= 0.280 Angle : 0.759 12.671 12163 Z= 0.383 Chirality : 0.047 0.210 1377 Planarity : 0.005 0.061 1511 Dihedral : 7.867 57.657 1276 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.13 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1091 helix: 0.91 (0.28), residues: 356 sheet: 0.04 (0.33), residues: 251 loop : -1.62 (0.27), residues: 484 =============================================================================== Job complete usr+sys time: 2301.19 seconds wall clock time: 42 minutes 39.58 seconds (2559.58 seconds total)