Starting phenix.real_space_refine on Wed Feb 14 06:29:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d77_30603/02_2024/7d77_30603.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d77_30603/02_2024/7d77_30603.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_30603/02_2024/7d77_30603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d77_30603/02_2024/7d77_30603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d77_30603/02_2024/7d77_30603.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d77_30603/02_2024/7d77_30603.pdb" } resolution = 2.9 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= 0.014 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 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. 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-5238/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: 5.48, per 1000 atoms: 0.62 Number of scatterers: 8785 At special positions: 0 Unit cell: (105.456, 126.75, 112.554, 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 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: 1.05 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: 2.85 Time building geometry restraints manager: 3.54 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: 5114 21.33 - 42.66: 323 42.66 - 63.99: 32 63.99 - 85.32: 10 85.32 - 106.65: 2 Dihedral angle restraints: 5481 sinusoidal: 2302 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 5478 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 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: 0.580 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: 2.050 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.070 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 13.717 106.650 3435 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 % Allowed : 4.83 % Favored : 94.95 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 339 HIS 0.008 0.001 HIS R 309 PHE 0.016 0.002 PHE A 190 TYR 0.015 0.002 TYR S 178 ARG 0.003 0.000 ARG B 49 *********************** 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 140 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7774 (ttp80) REVERT: B 124 TYR cc_start: 0.8912 (m-80) cc_final: 0.8592 (m-80) REVERT: B 130 GLU cc_start: 0.7681 (mp0) cc_final: 0.7465 (mp0) REVERT: B 138 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8475 (mt-10) REVERT: B 153 ASP cc_start: 0.7626 (m-30) cc_final: 0.7394 (m-30) REVERT: R 447 MET cc_start: 0.6609 (mmt) cc_final: 0.6388 (mpt) REVERT: S 168 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7522 (mtt90) REVERT: S 174 GLN cc_start: 0.8810 (pt0) cc_final: 0.8591 (pt0) REVERT: S 194 SER cc_start: 0.8264 (t) cc_final: 0.8025 (p) outliers start: 2 outliers final: 1 residues processed: 140 average time/residue: 1.3909 time to fit residues: 206.0155 Evaluate side-chains 97 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN R 362 HIS S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8977 Z= 0.268 Angle : 0.570 7.692 12163 Z= 0.295 Chirality : 0.043 0.148 1377 Planarity : 0.003 0.038 1511 Dihedral : 7.601 58.889 1508 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.58 % Allowed : 11.28 % Favored : 86.14 % 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: -1.26 (0.24), residues: 1091 helix: 1.22 (0.27), residues: 355 sheet: -1.49 (0.28), residues: 274 loop : -2.05 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.006 0.001 HIS R 309 PHE 0.021 0.001 PHE R 285 TYR 0.029 0.001 TYR B 105 ARG 0.004 0.000 ARG S 148 *********************** 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 133 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.042 Fit side-chains REVERT: A 28 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7975 (mp) REVERT: A 43 ASN cc_start: 0.7459 (t0) cc_final: 0.7183 (t0) REVERT: A 248 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7286 (tt) REVERT: B 19 ARG cc_start: 0.7960 (ttp-110) cc_final: 0.7740 (ttp80) REVERT: B 130 GLU cc_start: 0.7584 (mp0) cc_final: 0.7317 (mp0) REVERT: B 138 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8281 (mt-10) REVERT: B 214 ARG cc_start: 0.7594 (mpt90) cc_final: 0.7356 (mpt90) REVERT: S 109 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8116 (p0) outliers start: 24 outliers final: 13 residues processed: 122 average time/residue: 1.1735 time to fit residues: 153.8078 Evaluate side-chains 116 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 109 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.7655 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8977 Z= 0.204 Angle : 0.521 7.427 12163 Z= 0.271 Chirality : 0.041 0.139 1377 Planarity : 0.003 0.035 1511 Dihedral : 7.243 59.590 1508 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.69 % Allowed : 13.96 % Favored : 83.35 % 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: -0.63 (0.25), residues: 1091 helix: 1.82 (0.28), residues: 355 sheet: -1.14 (0.28), residues: 274 loop : -1.77 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS R 309 PHE 0.021 0.001 PHE R 292 TYR 0.018 0.001 TYR B 105 ARG 0.002 0.000 ARG A 349 *********************** 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 128 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.939 Fit side-chains REVERT: A 28 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7847 (mp) REVERT: A 43 ASN cc_start: 0.7410 (t0) cc_final: 0.7104 (t0) REVERT: A 54 LYS cc_start: 0.6639 (mtmt) cc_final: 0.6379 (tmtm) REVERT: A 307 GLN cc_start: 0.8036 (tt0) cc_final: 0.7818 (tt0) REVERT: B 138 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 175 GLN cc_start: 0.8266 (mm110) cc_final: 0.7824 (mm110) REVERT: B 217 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6439 (ptt) REVERT: S 109 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8105 (p0) outliers start: 25 outliers final: 13 residues processed: 117 average time/residue: 1.1181 time to fit residues: 140.9617 Evaluate side-chains 120 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.7674 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8977 Z= 0.287 Angle : 0.551 8.035 12163 Z= 0.285 Chirality : 0.043 0.188 1377 Planarity : 0.003 0.036 1511 Dihedral : 7.202 59.947 1508 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.11 % Allowed : 15.68 % Favored : 81.20 % 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: -0.46 (0.25), residues: 1091 helix: 1.89 (0.28), residues: 360 sheet: -0.97 (0.28), residues: 274 loop : -1.69 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS A 214 PHE 0.024 0.002 PHE R 285 TYR 0.018 0.001 TYR B 105 ARG 0.003 0.000 ARG A 349 *********************** 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 137 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 1.065 Fit side-chains REVERT: A 28 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7865 (mp) REVERT: A 43 ASN cc_start: 0.7370 (t0) cc_final: 0.7061 (t0) REVERT: B 130 GLU cc_start: 0.7557 (mp0) cc_final: 0.7355 (mp0) REVERT: B 138 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8166 (mt-10) REVERT: B 175 GLN cc_start: 0.8298 (mm110) cc_final: 0.7867 (mm110) REVERT: B 217 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6410 (ptt) REVERT: S 109 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8113 (p0) REVERT: S 190 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7152 (mtm110) outliers start: 29 outliers final: 20 residues processed: 125 average time/residue: 1.3217 time to fit residues: 175.8063 Evaluate side-chains 129 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 190 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.0570 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- 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: 0.7622 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8977 Z= 0.148 Angle : 0.489 8.659 12163 Z= 0.253 Chirality : 0.040 0.214 1377 Planarity : 0.003 0.034 1511 Dihedral : 6.646 59.778 1508 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.58 % Allowed : 17.19 % Favored : 80.24 % 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: -0.04 (0.25), residues: 1091 helix: 2.27 (0.28), residues: 360 sheet: -0.64 (0.29), residues: 273 loop : -1.55 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS R 309 PHE 0.027 0.001 PHE R 292 TYR 0.012 0.001 TYR S 178 ARG 0.008 0.000 ARG B 19 *********************** 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 148 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 0.924 Fit side-chains REVERT: A 43 ASN cc_start: 0.7405 (t0) cc_final: 0.7189 (t0) REVERT: B 138 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8097 (mt-10) REVERT: B 175 GLN cc_start: 0.8324 (mm110) cc_final: 0.8063 (mm110) outliers start: 24 outliers final: 14 residues processed: 136 average time/residue: 1.1930 time to fit residues: 173.3402 Evaluate side-chains 127 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain R residue 447 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.0060 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8977 Z= 0.141 Angle : 0.479 8.663 12163 Z= 0.247 Chirality : 0.040 0.182 1377 Planarity : 0.003 0.036 1511 Dihedral : 6.313 59.203 1508 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.11 % Allowed : 17.19 % Favored : 79.70 % 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: 0.20 (0.25), residues: 1091 helix: 2.45 (0.28), residues: 360 sheet: -0.36 (0.30), residues: 259 loop : -1.47 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS R 309 PHE 0.025 0.001 PHE R 516 TYR 0.011 0.001 TYR S 178 ARG 0.009 0.000 ARG B 197 *********************** 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 144 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 1.049 Fit side-chains REVERT: A 43 ASN cc_start: 0.7482 (t0) cc_final: 0.7278 (t0) REVERT: A 210 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7902 (pttp) REVERT: B 129 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7407 (tpt90) REVERT: B 138 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8092 (mt-10) REVERT: B 175 GLN cc_start: 0.8314 (mm110) cc_final: 0.8054 (mm110) outliers start: 29 outliers final: 13 residues processed: 134 average time/residue: 1.1703 time to fit residues: 167.8711 Evaluate side-chains 126 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain R residue 447 MET Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 104 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8977 Z= 0.224 Angle : 0.519 9.081 12163 Z= 0.268 Chirality : 0.042 0.199 1377 Planarity : 0.003 0.050 1511 Dihedral : 6.447 59.098 1508 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.58 % Allowed : 18.37 % Favored : 79.05 % 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: 0.23 (0.26), residues: 1091 helix: 2.40 (0.28), residues: 360 sheet: -0.41 (0.30), residues: 270 loop : -1.35 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.029 0.001 PHE R 292 TYR 0.012 0.001 TYR S 178 ARG 0.011 0.000 ARG B 197 *********************** 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 136 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.014 Fit side-chains REVERT: B 138 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 175 GLN cc_start: 0.8239 (mm110) cc_final: 0.7933 (mm110) REVERT: R 300 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7736 (m-80) outliers start: 24 outliers final: 18 residues processed: 128 average time/residue: 1.2417 time to fit residues: 169.4548 Evaluate side-chains 119 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 300 PHE Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain R residue 447 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.7640 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8977 Z= 0.208 Angle : 0.525 9.310 12163 Z= 0.275 Chirality : 0.042 0.274 1377 Planarity : 0.003 0.045 1511 Dihedral : 6.379 59.287 1508 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.90 % Allowed : 18.58 % Favored : 78.52 % 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: 0.31 (0.25), residues: 1091 helix: 2.41 (0.28), residues: 360 sheet: -0.27 (0.30), residues: 264 loop : -1.31 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 339 HIS 0.003 0.001 HIS S 35 PHE 0.026 0.001 PHE R 516 TYR 0.011 0.001 TYR S 178 ARG 0.011 0.000 ARG B 197 *********************** 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 130 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 1.027 Fit side-chains REVERT: A 210 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7931 (pttp) REVERT: B 138 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8066 (mt-10) REVERT: B 175 GLN cc_start: 0.8237 (mm110) cc_final: 0.7918 (mm110) REVERT: B 217 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6554 (ptt) REVERT: S 83 MET cc_start: 0.8784 (mtm) cc_final: 0.8408 (mpp) outliers start: 27 outliers final: 18 residues processed: 119 average time/residue: 1.0974 time to fit residues: 140.5670 Evaluate side-chains 130 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain R residue 447 MET Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 0.0270 chunk 42 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- 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: 0.7643 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8977 Z= 0.216 Angle : 0.531 9.417 12163 Z= 0.277 Chirality : 0.042 0.254 1377 Planarity : 0.004 0.055 1511 Dihedral : 6.376 59.283 1508 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.69 % Allowed : 19.23 % Favored : 78.09 % 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: 0.34 (0.25), residues: 1091 helix: 2.41 (0.28), residues: 360 sheet: -0.24 (0.30), residues: 264 loop : -1.27 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.034 0.001 PHE R 292 TYR 0.011 0.001 TYR S 178 ARG 0.014 0.000 ARG B 197 *********************** 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 136 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.952 Fit side-chains REVERT: A 210 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7926 (pttp) REVERT: B 138 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8034 (mt-10) REVERT: B 175 GLN cc_start: 0.8270 (mm110) cc_final: 0.7950 (mm110) REVERT: B 217 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6563 (ptt) REVERT: R 300 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: S 43 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8005 (mttm) outliers start: 25 outliers final: 22 residues processed: 125 average time/residue: 1.2319 time to fit residues: 164.5001 Evaluate side-chains 136 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 300 PHE Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain R residue 447 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2038 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 : 0.527 9.867 12163 Z= 0.272 Chirality : 0.042 0.285 1377 Planarity : 0.003 0.054 1511 Dihedral : 6.252 59.263 1508 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.26 % Allowed : 20.19 % Favored : 77.55 % 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: 0.43 (0.26), residues: 1091 helix: 2.46 (0.28), residues: 360 sheet: -0.04 (0.30), residues: 266 loop : -1.31 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS S 35 PHE 0.027 0.001 PHE R 516 TYR 0.011 0.001 TYR B 124 ARG 0.011 0.000 ARG B 197 ********************** 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 131 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.021 Fit side-chains REVERT: A 210 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7909 (pttp) REVERT: B 42 ARG cc_start: 0.7399 (ttp80) cc_final: 0.7127 (tmt170) REVERT: B 138 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7992 (mt-10) REVERT: B 175 GLN cc_start: 0.8285 (mm110) cc_final: 0.7970 (mm110) REVERT: B 219 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7501 (mtt-85) REVERT: S 43 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8010 (mttm) outliers start: 21 outliers final: 17 residues processed: 121 average time/residue: 1.2364 time to fit residues: 159.7056 Evaluate side-chains 128 residues out of total 931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain R residue 447 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119225 restraints weight = 9866.554| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.32 r_work: 0.3097 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8977 Z= 0.258 Angle : 0.560 9.715 12163 Z= 0.289 Chirality : 0.043 0.292 1377 Planarity : 0.004 0.080 1511 Dihedral : 6.470 59.431 1508 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.69 % Allowed : 19.55 % Favored : 77.77 % 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 (0.26), residues: 1091 helix: 2.37 (0.28), residues: 360 sheet: -0.21 (0.30), residues: 264 loop : -1.22 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.034 0.001 PHE R 292 TYR 0.012 0.001 TYR S 178 ARG 0.020 0.001 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3436.58 seconds wall clock time: 61 minutes 56.46 seconds (3716.46 seconds total)