Starting phenix.real_space_refine on Sat Apr 6 13:39:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lci_23274/04_2024/7lci_23274_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lci_23274/04_2024/7lci_23274.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/7lci_23274/04_2024/7lci_23274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lci_23274/04_2024/7lci_23274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lci_23274/04_2024/7lci_23274_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lci_23274/04_2024/7lci_23274_updated.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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 5297 2.51 5 N 1437 2.21 5 O 1532 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 52": "OE1" <-> "OE2" Residue "R PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R GLU 125": "OE1" <-> "OE2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 376": "NH1" <-> "NH2" Residue "R GLU 418": "OE1" <-> "OE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8317 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3241 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2006 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2573 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 60 Unusual residues: {'UK4': 1} Classifications: {'undetermined': 1, 'water': 19} Link IDs: {None: 19} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.81, per 1000 atoms: 0.58 Number of scatterers: 8317 At special positions: 0 Unit cell: (146.91, 102.09, 112.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 F 1 9.00 O 1532 8.00 N 1437 7.00 C 5297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.02 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 9 sheets defined 40.9% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'R' and resid 32 through 52 removed outlier: 3.679A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 168 removed outlier: 3.854A pdb=" N PHE R 143 " --> pdb=" O GLU R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 200 Processing helix chain 'R' and resid 206 through 208 No H-bonds generated for 'chain 'R' and resid 206 through 208' Processing helix chain 'R' and resid 211 through 221 removed outlier: 4.311A pdb=" N ASP R 215 " --> pdb=" O HIS R 212 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY R 216 " --> pdb=" O GLN R 213 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR R 220 " --> pdb=" O LEU R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 255 Processing helix chain 'R' and resid 262 through 275 removed outlier: 3.757A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 290 removed outlier: 3.516A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 306 through 337 removed outlier: 3.516A pdb=" N ARG R 310 " --> pdb=" O LEU R 307 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU R 311 " --> pdb=" O ILE R 308 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 342 through 360 removed outlier: 4.078A pdb=" N LYS R 346 " --> pdb=" O LYS R 342 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 364 No H-bonds generated for 'chain 'R' and resid 362 through 364' Processing helix chain 'R' and resid 366 through 369 No H-bonds generated for 'chain 'R' and resid 366 through 369' Processing helix chain 'R' and resid 378 through 402 removed outlier: 3.533A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLN R 394 " --> pdb=" O PHE R 390 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 422 removed outlier: 4.337A pdb=" N TRP R 420 " --> pdb=" O SER R 416 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG R 421 " --> pdb=" O TRP R 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 37 removed outlier: 3.509A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.507A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.612A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 44 removed outlier: 4.024A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'R' and resid 79 through 84 removed outlier: 3.663A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG R 102 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 removed outlier: 3.741A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 92 through 94 removed outlier: 3.865A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.632A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.651A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.212A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.466A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.745A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.734A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 975 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: 2.21 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1346 1.27 - 1.40: 2242 1.40 - 1.54: 4800 1.54 - 1.68: 36 1.68 - 1.81: 68 Bond restraints: 8492 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.421 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.526 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C28 UK4 R 501 " pdb=" C29 UK4 R 501 " ideal model delta sigma weight residual 1.529 1.448 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" N VAL A 256 " pdb=" CA VAL A 256 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.32e-02 5.74e+03 9.03e+00 bond pdb=" C06 UK4 R 501 " pdb=" O05 UK4 R 501 " ideal model delta sigma weight residual 1.345 1.405 -0.060 2.00e-02 2.50e+03 8.86e+00 ... (remaining 8487 not shown) Histogram of bond angle deviations from ideal: 89.52 - 107.59: 301 107.59 - 125.67: 11044 125.67 - 143.74: 173 143.74 - 161.82: 0 161.82 - 179.89: 1 Bond angle restraints: 11519 Sorted by residual: angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 111.07 118.18 -7.11 1.07e+00 8.73e-01 4.41e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 91.95 18.31 3.00e+00 1.11e-01 3.72e+01 angle pdb=" N ASP R 344 " pdb=" CA ASP R 344 " pdb=" C ASP R 344 " ideal model delta sigma weight residual 111.28 105.00 6.28 1.09e+00 8.42e-01 3.32e+01 angle pdb=" CA ILE A 257 " pdb=" C ILE A 257 " pdb=" O ILE A 257 " ideal model delta sigma weight residual 122.63 117.81 4.82 8.70e-01 1.32e+00 3.07e+01 angle pdb=" N VAL R 365 " pdb=" CA VAL R 365 " pdb=" C VAL R 365 " ideal model delta sigma weight residual 111.81 107.10 4.71 8.60e-01 1.35e+00 3.00e+01 ... (remaining 11514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4559 17.95 - 35.90: 403 35.90 - 53.86: 51 53.86 - 71.81: 6 71.81 - 89.76: 9 Dihedral angle restraints: 5028 sinusoidal: 2007 harmonic: 3021 Sorted by residual: dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -120.92 34.92 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" C ASP R 344 " pdb=" N ASP R 344 " pdb=" CA ASP R 344 " pdb=" CB ASP R 344 " ideal model delta harmonic sigma weight residual -122.60 -112.30 -10.30 0 2.50e+00 1.60e-01 1.70e+01 ... (remaining 5025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1123 0.072 - 0.144: 127 0.144 - 0.216: 14 0.216 - 0.288: 4 0.288 - 0.360: 1 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA ASP R 344 " pdb=" N ASP R 344 " pdb=" C ASP R 344 " pdb=" CB ASP R 344 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU R 339 " pdb=" N LEU R 339 " pdb=" C LEU R 339 " pdb=" CB LEU R 339 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1266 not shown) Planarity restraints: 1462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO G 53 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 306 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C SER A 306 " -0.050 2.00e-02 2.50e+03 pdb=" O SER A 306 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 307 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER R 136 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO R 137 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO R 137 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 137 " -0.031 5.00e-02 4.00e+02 ... (remaining 1459 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 747 2.74 - 3.28: 8484 3.28 - 3.82: 13841 3.82 - 4.36: 17211 4.36 - 4.90: 29054 Nonbonded interactions: 69337 Sorted by model distance: nonbonded pdb=" OD1 ASN R 300 " pdb=" N SER R 301 " model vdw 2.203 2.520 nonbonded pdb=" NH2 ARG R 40 " pdb=" OD2 ASP R 222 " model vdw 2.243 2.520 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.245 2.520 nonbonded pdb=" NZ LYS R 113 " pdb=" O LEU R 118 " model vdw 2.256 2.520 nonbonded pdb=" OD2 ASP R 67 " pdb=" NH1 ARG R 121 " model vdw 2.276 2.520 ... (remaining 69332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 5.640 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.970 Find NCS groups from input model: 0.230 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:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 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 : 0.005 0.114 8492 Z= 0.305 Angle : 0.784 18.306 11519 Z= 0.475 Chirality : 0.050 0.360 1269 Planarity : 0.004 0.084 1462 Dihedral : 13.609 89.759 3058 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 1020 helix: -0.13 (0.25), residues: 437 sheet: -0.56 (0.37), residues: 183 loop : -1.13 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 243 HIS 0.005 0.001 HIS R 180 PHE 0.016 0.002 PHE R 280 TYR 0.017 0.002 TYR B 59 ARG 0.009 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: R 88 TYR cc_start: 0.7010 (p90) cc_final: 0.6511 (p90) REVERT: R 393 PHE cc_start: 0.6826 (m-80) cc_final: 0.6497 (m-80) REVERT: A 208 PHE cc_start: 0.7260 (t80) cc_final: 0.6795 (m-80) REVERT: A 255 MET cc_start: 0.5990 (mtp) cc_final: 0.5764 (mtp) REVERT: A 372 ILE cc_start: 0.7550 (mt) cc_final: 0.7217 (pt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 1.0558 time to fit residues: 181.0386 Evaluate side-chains 96 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 0.0470 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN A 31 GLN A 35 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8492 Z= 0.210 Angle : 0.591 10.205 11519 Z= 0.315 Chirality : 0.043 0.176 1269 Planarity : 0.005 0.049 1462 Dihedral : 5.017 25.064 1154 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.61 % Allowed : 11.00 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1020 helix: 0.59 (0.25), residues: 440 sheet: -0.03 (0.37), residues: 177 loop : -0.95 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.008 0.002 HIS A 357 PHE 0.018 0.002 PHE B 151 TYR 0.034 0.002 TYR R 148 ARG 0.010 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.917 Fit side-chains REVERT: R 88 TYR cc_start: 0.7049 (p90) cc_final: 0.6642 (p90) REVERT: R 286 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7408 (mm) REVERT: R 294 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.5716 (mm-30) REVERT: R 393 PHE cc_start: 0.7040 (m-80) cc_final: 0.6578 (m-80) REVERT: A 255 MET cc_start: 0.6006 (mtp) cc_final: 0.5788 (mtp) REVERT: A 309 GLU cc_start: 0.5180 (OUTLIER) cc_final: 0.4864 (mp0) REVERT: B 153 ASP cc_start: 0.6032 (t0) cc_final: 0.5815 (t70) outliers start: 23 outliers final: 15 residues processed: 119 average time/residue: 0.9983 time to fit residues: 128.5446 Evaluate side-chains 104 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN A 12 GLN A 35 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8492 Z= 0.392 Angle : 0.720 10.863 11519 Z= 0.380 Chirality : 0.048 0.191 1269 Planarity : 0.006 0.064 1462 Dihedral : 5.568 30.946 1154 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.85 % Allowed : 14.17 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.39 (0.26), residues: 1020 helix: 0.30 (0.25), residues: 438 sheet: -0.20 (0.39), residues: 171 loop : -0.76 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP R 420 HIS 0.014 0.002 HIS R 180 PHE 0.035 0.003 PHE B 151 TYR 0.034 0.003 TYR R 148 ARG 0.007 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 294 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.5368 (mm-30) REVERT: R 351 LYS cc_start: 0.7376 (tttt) cc_final: 0.6854 (mttm) REVERT: R 420 TRP cc_start: 0.5225 (OUTLIER) cc_final: 0.5016 (m-90) REVERT: A 283 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6416 (mtm180) REVERT: A 309 GLU cc_start: 0.5382 (OUTLIER) cc_final: 0.5089 (mp0) REVERT: A 372 ILE cc_start: 0.8090 (mp) cc_final: 0.7851 (mp) REVERT: B 239 ASN cc_start: 0.6225 (m110) cc_final: 0.5953 (t0) REVERT: B 325 MET cc_start: 0.7259 (mmm) cc_final: 0.6642 (mmm) REVERT: B 339 TRP cc_start: 0.6348 (m100) cc_final: 0.6051 (m-10) outliers start: 34 outliers final: 18 residues processed: 122 average time/residue: 1.0705 time to fit residues: 140.3246 Evaluate side-chains 112 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 420 TRP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 410 GLN A 12 GLN A 35 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8492 Z= 0.172 Angle : 0.539 9.170 11519 Z= 0.287 Chirality : 0.042 0.169 1269 Planarity : 0.004 0.044 1462 Dihedral : 4.894 26.924 1154 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.63 % Allowed : 17.01 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 1020 helix: 0.98 (0.26), residues: 433 sheet: 0.04 (0.38), residues: 179 loop : -0.70 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 420 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE B 241 TYR 0.027 0.002 TYR R 148 ARG 0.004 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 91 time to evaluate : 0.901 Fit side-chains REVERT: R 88 TYR cc_start: 0.7024 (p90) cc_final: 0.6660 (p90) REVERT: R 286 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7440 (mm) REVERT: R 294 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.4893 (mm-30) REVERT: A 271 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6381 (ptmt) REVERT: A 283 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6292 (mtm180) REVERT: A 311 TYR cc_start: 0.5724 (m-80) cc_final: 0.5032 (t80) REVERT: B 325 MET cc_start: 0.7178 (mmm) cc_final: 0.6680 (mmm) outliers start: 32 outliers final: 15 residues processed: 108 average time/residue: 1.0008 time to fit residues: 116.7076 Evaluate side-chains 101 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8492 Z= 0.160 Angle : 0.525 7.584 11519 Z= 0.280 Chirality : 0.041 0.162 1269 Planarity : 0.004 0.043 1462 Dihedral : 4.751 25.552 1154 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.17 % Allowed : 18.37 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1020 helix: 1.28 (0.26), residues: 433 sheet: 0.22 (0.38), residues: 175 loop : -0.66 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.001 PHE B 241 TYR 0.027 0.002 TYR R 148 ARG 0.008 0.000 ARG R 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: R 88 TYR cc_start: 0.7006 (p90) cc_final: 0.6633 (p90) REVERT: R 294 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.4768 (mm-30) REVERT: R 369 PHE cc_start: 0.6649 (m-10) cc_final: 0.6434 (m-10) REVERT: A 208 PHE cc_start: 0.7361 (t80) cc_final: 0.6532 (m-80) REVERT: A 271 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6358 (ptmt) REVERT: A 283 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6292 (mtm180) REVERT: A 311 TYR cc_start: 0.5825 (m-80) cc_final: 0.5201 (t80) REVERT: A 372 ILE cc_start: 0.8124 (mp) cc_final: 0.7868 (mp) REVERT: B 325 MET cc_start: 0.7085 (mmm) cc_final: 0.6692 (mmm) outliers start: 28 outliers final: 15 residues processed: 110 average time/residue: 1.0613 time to fit residues: 125.6684 Evaluate side-chains 102 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN B 75 GLN B 88 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8492 Z= 0.313 Angle : 0.647 8.957 11519 Z= 0.344 Chirality : 0.046 0.181 1269 Planarity : 0.005 0.047 1462 Dihedral : 5.249 29.187 1154 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.31 % Allowed : 18.14 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.27), residues: 1020 helix: 0.94 (0.26), residues: 433 sheet: -0.10 (0.37), residues: 182 loop : -0.77 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 243 HIS 0.008 0.002 HIS A 357 PHE 0.030 0.002 PHE B 151 TYR 0.030 0.003 TYR R 148 ARG 0.007 0.001 ARG R 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 93 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: R 286 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7473 (mm) REVERT: R 294 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5308 (mm-30) REVERT: R 351 LYS cc_start: 0.7340 (tttt) cc_final: 0.6775 (mttm) REVERT: A 271 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6414 (ptmt) REVERT: A 283 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6351 (mtm180) REVERT: A 311 TYR cc_start: 0.5995 (m-80) cc_final: 0.5300 (t80) REVERT: A 372 ILE cc_start: 0.8135 (mp) cc_final: 0.7895 (mp) REVERT: B 325 MET cc_start: 0.7148 (mmm) cc_final: 0.6611 (mmm) outliers start: 38 outliers final: 19 residues processed: 115 average time/residue: 0.9963 time to fit residues: 124.0140 Evaluate side-chains 111 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8492 Z= 0.158 Angle : 0.534 7.634 11519 Z= 0.288 Chirality : 0.042 0.158 1269 Planarity : 0.004 0.042 1462 Dihedral : 4.799 25.694 1154 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.06 % Allowed : 20.52 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1020 helix: 1.30 (0.26), residues: 434 sheet: 0.12 (0.38), residues: 182 loop : -0.65 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.022 0.001 PHE B 241 TYR 0.026 0.002 TYR R 148 ARG 0.008 0.000 ARG R 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: R 88 TYR cc_start: 0.6920 (p90) cc_final: 0.6500 (p90) REVERT: R 294 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.4818 (mm-30) REVERT: A 208 PHE cc_start: 0.7332 (t80) cc_final: 0.6367 (m-80) REVERT: A 271 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6337 (ptmt) REVERT: A 283 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6261 (mtm180) REVERT: A 311 TYR cc_start: 0.5852 (m-80) cc_final: 0.5329 (t80) REVERT: A 372 ILE cc_start: 0.8138 (mp) cc_final: 0.7909 (mp) REVERT: B 325 MET cc_start: 0.7091 (mmm) cc_final: 0.6574 (mmm) outliers start: 27 outliers final: 18 residues processed: 104 average time/residue: 0.9486 time to fit residues: 106.9836 Evaluate side-chains 101 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8492 Z= 0.159 Angle : 0.539 9.080 11519 Z= 0.288 Chirality : 0.042 0.160 1269 Planarity : 0.004 0.046 1462 Dihedral : 4.692 24.717 1154 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.63 % Allowed : 19.50 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 1020 helix: 1.38 (0.26), residues: 434 sheet: 0.20 (0.38), residues: 182 loop : -0.58 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.022 0.001 PHE B 241 TYR 0.025 0.002 TYR R 148 ARG 0.008 0.000 ARG R 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 85 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: R 294 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.4803 (mm-30) REVERT: A 208 PHE cc_start: 0.7320 (t80) cc_final: 0.6380 (m-80) REVERT: A 271 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6327 (ptmt) REVERT: A 283 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6271 (mtm180) REVERT: A 311 TYR cc_start: 0.5835 (m-80) cc_final: 0.5340 (t80) REVERT: A 339 TYR cc_start: 0.7222 (m-80) cc_final: 0.6934 (m-80) REVERT: A 372 ILE cc_start: 0.8133 (mp) cc_final: 0.7912 (mp) REVERT: B 325 MET cc_start: 0.7089 (mmm) cc_final: 0.6521 (mmm) outliers start: 32 outliers final: 20 residues processed: 105 average time/residue: 0.9394 time to fit residues: 107.0915 Evaluate side-chains 104 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8492 Z= 0.272 Angle : 0.622 9.119 11519 Z= 0.332 Chirality : 0.045 0.172 1269 Planarity : 0.005 0.081 1462 Dihedral : 5.094 27.521 1154 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.63 % Allowed : 19.61 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 1020 helix: 1.22 (0.26), residues: 433 sheet: -0.00 (0.38), residues: 182 loop : -0.71 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.003 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.028 0.002 PHE B 151 TYR 0.030 0.002 TYR B 59 ARG 0.013 0.001 ARG R 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: R 294 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5162 (mm-30) REVERT: R 336 LYS cc_start: 0.6011 (mtpt) cc_final: 0.5623 (mptp) REVERT: A 208 PHE cc_start: 0.7370 (t80) cc_final: 0.6354 (m-80) REVERT: A 271 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6394 (ptmt) REVERT: A 283 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6323 (mtm180) REVERT: A 311 TYR cc_start: 0.5868 (m-80) cc_final: 0.5387 (t80) REVERT: B 239 ASN cc_start: 0.6372 (m110) cc_final: 0.6020 (m-40) REVERT: B 325 MET cc_start: 0.7074 (mmm) cc_final: 0.6658 (mmm) outliers start: 32 outliers final: 23 residues processed: 104 average time/residue: 0.9024 time to fit residues: 102.6052 Evaluate side-chains 106 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 8492 Z= 0.483 Angle : 0.794 10.557 11519 Z= 0.422 Chirality : 0.052 0.198 1269 Planarity : 0.007 0.089 1462 Dihedral : 5.917 32.576 1154 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.29 % Allowed : 20.63 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.41 (0.26), residues: 1020 helix: 0.46 (0.25), residues: 434 sheet: -0.28 (0.40), residues: 163 loop : -0.94 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.136 0.004 TRP B 339 HIS 0.013 0.003 HIS A 357 PHE 0.045 0.003 PHE B 151 TYR 0.052 0.004 TYR B 59 ARG 0.013 0.001 ARG R 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 0.930 Fit side-chains REVERT: R 170 ARG cc_start: 0.6435 (ttm-80) cc_final: 0.5958 (tpt90) REVERT: R 286 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7524 (mm) REVERT: R 294 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.5469 (mm-30) REVERT: R 348 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.5517 (tmt-80) REVERT: A 271 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6413 (ptmt) REVERT: A 283 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6355 (mtm180) REVERT: A 311 TYR cc_start: 0.6012 (m-80) cc_final: 0.5430 (t80) REVERT: B 325 MET cc_start: 0.7134 (mmm) cc_final: 0.6690 (mmm) outliers start: 29 outliers final: 17 residues processed: 106 average time/residue: 0.9903 time to fit residues: 113.7767 Evaluate side-chains 105 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 264 TRP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.221052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.185834 restraints weight = 9575.965| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 1.77 r_work: 0.4009 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8492 Z= 0.182 Angle : 0.596 9.787 11519 Z= 0.318 Chirality : 0.043 0.164 1269 Planarity : 0.004 0.061 1462 Dihedral : 5.169 28.151 1154 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.06 % Allowed : 21.43 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 1020 helix: 1.07 (0.26), residues: 432 sheet: -0.06 (0.38), residues: 181 loop : -0.86 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.003 TRP B 339 HIS 0.003 0.001 HIS B 62 PHE 0.020 0.002 PHE B 241 TYR 0.027 0.002 TYR R 148 ARG 0.012 0.000 ARG R 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3033.54 seconds wall clock time: 55 minutes 19.59 seconds (3319.59 seconds total)