Starting phenix.real_space_refine on Sat Apr 6 12:05:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6d_36001/04_2024/8j6d_36001.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6d_36001/04_2024/8j6d_36001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6d_36001/04_2024/8j6d_36001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6d_36001/04_2024/8j6d_36001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6d_36001/04_2024/8j6d_36001.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6d_36001/04_2024/8j6d_36001.pdb" } resolution = 3.1 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= 0.005 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5197 2.51 5 N 1401 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "H ASP 137": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8149 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1578 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2402 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2027 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 14, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Chain: "D" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 73 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 386 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1683 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 4.78, per 1000 atoms: 0.59 Number of scatterers: 8149 At special positions: 0 Unit cell: (85.1, 118.45, 123.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1497 8.00 N 1401 7.00 C 5197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " 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=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.7% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.668A pdb=" N GLU A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.351A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.043A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.954A pdb=" N ALA A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.545A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 20 through 50 removed outlier: 3.847A pdb=" N VAL C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) Proline residue: C 39 - end of helix Processing helix chain 'C' and resid 55 through 85 removed outlier: 4.408A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 91 through 126 Proline residue: C 99 - end of helix removed outlier: 3.826A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 135 through 154 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 332 through 363 removed outlier: 3.738A pdb=" N THR C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 364 through 370 removed outlier: 6.842A pdb=" N ARG C 367 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS C 370 " --> pdb=" O ARG C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 403 removed outlier: 3.814A pdb=" N PHE C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Proline residue: C 392 - end of helix removed outlier: 4.075A pdb=" N GLY C 397 " --> pdb=" O TYR C 393 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 398 " --> pdb=" O HIS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 436 removed outlier: 4.750A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 439 through 448 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 53 through 56 removed outlier: 4.273A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 3.561A pdb=" N ASP A 201 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.557A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.890A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.982A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.965A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.571A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.000A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.333A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 163 through 164 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.674A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.632A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 5.948A pdb=" N VAL H 147 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1248 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: 2.41 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1987 1.33 - 1.45: 1730 1.45 - 1.57: 4537 1.57 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 8325 Sorted by residual: bond pdb=" N ASP G 48 " pdb=" CA ASP G 48 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.06e-02 8.90e+03 7.36e+00 bond pdb=" C GLY C 439 " pdb=" O GLY C 439 " ideal model delta sigma weight residual 1.231 1.266 -0.035 1.33e-02 5.65e+03 6.94e+00 bond pdb=" N ARG D 69 " pdb=" CA ARG D 69 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.32e-02 5.74e+03 6.59e+00 bond pdb=" N THR C 331 " pdb=" CA THR C 331 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.90e-02 2.77e+03 6.33e+00 bond pdb=" C ARG C 443 " pdb=" O ARG C 443 " ideal model delta sigma weight residual 1.236 1.263 -0.027 1.15e-02 7.56e+03 5.44e+00 ... (remaining 8320 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.72: 210 106.72 - 113.53: 4622 113.53 - 120.35: 3004 120.35 - 127.17: 3417 127.17 - 133.98: 100 Bond angle restraints: 11353 Sorted by residual: angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 111.62 107.06 4.56 7.90e-01 1.60e+00 3.34e+01 angle pdb=" CA THR C 331 " pdb=" C THR C 331 " pdb=" N PRO C 332 " ideal model delta sigma weight residual 116.90 124.14 -7.24 1.50e+00 4.44e-01 2.33e+01 angle pdb=" C ARG D 69 " pdb=" CA ARG D 69 " pdb=" CB ARG D 69 " ideal model delta sigma weight residual 110.11 101.37 8.74 1.90e+00 2.77e-01 2.12e+01 angle pdb=" C ILE C 29 " pdb=" N LEU C 30 " pdb=" CA LEU C 30 " ideal model delta sigma weight residual 120.58 112.87 7.71 1.71e+00 3.42e-01 2.03e+01 angle pdb=" CA LEU C 438 " pdb=" C LEU C 438 " pdb=" N GLY C 439 " ideal model delta sigma weight residual 118.41 112.42 5.99 1.34e+00 5.57e-01 2.00e+01 ... (remaining 11348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 4414 16.10 - 32.20: 353 32.20 - 48.30: 73 48.30 - 64.40: 11 64.40 - 80.50: 3 Dihedral angle restraints: 4854 sinusoidal: 1616 harmonic: 3238 Sorted by residual: dihedral pdb=" CA GLN C 364 " pdb=" C GLN C 364 " pdb=" N ARG C 365 " pdb=" CA ARG C 365 " ideal model delta harmonic sigma weight residual 180.00 -150.35 -29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLU A 8 " pdb=" C GLU A 8 " pdb=" N GLU A 9 " pdb=" CA GLU A 9 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ASP A 218 " pdb=" C ASP A 218 " pdb=" N VAL A 219 " pdb=" CA VAL A 219 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 4851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1098 0.057 - 0.113: 200 0.113 - 0.170: 30 0.170 - 0.227: 0 0.227 - 0.283: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA THR C 331 " pdb=" N THR C 331 " pdb=" C THR C 331 " pdb=" CB THR C 331 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA PHE C 164 " pdb=" N PHE C 164 " pdb=" C PHE C 164 " pdb=" CB PHE C 164 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA ARG D 69 " pdb=" N ARG D 69 " pdb=" C ARG D 69 " pdb=" CB ARG D 69 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1326 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 438 " 0.015 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU C 438 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU C 438 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY C 439 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 98 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO C 99 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 235 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO H 236 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 236 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 236 " -0.026 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 188 2.69 - 3.24: 8683 3.24 - 3.79: 12850 3.79 - 4.35: 17444 4.35 - 4.90: 29179 Nonbonded interactions: 68344 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.133 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.209 2.440 nonbonded pdb=" O ASN B 268 " pdb=" OD1 ASN B 268 " model vdw 2.251 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.252 2.440 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 177 " model vdw 2.255 2.440 ... (remaining 68339 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: 1.400 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: 5.360 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 25.210 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 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 : 0.004 0.048 8325 Z= 0.287 Angle : 0.730 9.114 11353 Z= 0.425 Chirality : 0.045 0.283 1329 Planarity : 0.005 0.052 1450 Dihedral : 12.635 80.495 2755 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.38 % Allowed : 11.93 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.02 (0.25), residues: 1103 helix: -0.39 (0.24), residues: 393 sheet: -0.52 (0.33), residues: 258 loop : -0.84 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 99 HIS 0.011 0.002 HIS B 311 PHE 0.018 0.002 PHE B 235 TYR 0.018 0.002 TYR C 393 ARG 0.011 0.001 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 145 TYR cc_start: 0.7754 (p90) cc_final: 0.7148 (p90) REVERT: C 90 TYR cc_start: 0.5293 (m-80) cc_final: 0.4851 (m-80) REVERT: C 412 THR cc_start: 0.7380 (m) cc_final: 0.6727 (m) REVERT: G 48 ASP cc_start: 0.7204 (t0) cc_final: 0.6950 (t0) REVERT: H 216 ILE cc_start: 0.8342 (mp) cc_final: 0.8108 (mt) outliers start: 3 outliers final: 3 residues processed: 176 average time/residue: 0.2307 time to fit residues: 53.3268 Evaluate side-chains 151 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain D residue 77 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.0020 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.0040 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 330 ASN B 32 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8325 Z= 0.191 Angle : 0.626 11.764 11353 Z= 0.320 Chirality : 0.043 0.238 1329 Planarity : 0.004 0.053 1450 Dihedral : 5.317 57.475 1199 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.03 % Allowed : 12.69 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.27 (0.25), residues: 1103 helix: 0.62 (0.26), residues: 399 sheet: -0.47 (0.32), residues: 251 loop : -0.59 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 169 HIS 0.003 0.001 HIS C 394 PHE 0.021 0.002 PHE A 192 TYR 0.014 0.001 TYR A 354 ARG 0.004 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: B 78 LYS cc_start: 0.8305 (mmmt) cc_final: 0.7896 (mmmt) REVERT: B 145 TYR cc_start: 0.7573 (p90) cc_final: 0.7188 (p90) REVERT: B 259 GLN cc_start: 0.6880 (tp40) cc_final: 0.6641 (mm110) REVERT: B 325 MET cc_start: 0.7293 (mmm) cc_final: 0.7061 (mmm) REVERT: C 35 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7723 (mm) REVERT: C 395 ILE cc_start: 0.7170 (pt) cc_final: 0.6826 (pt) REVERT: C 416 TRP cc_start: 0.7401 (m100) cc_final: 0.6823 (m100) REVERT: D 77 ARG cc_start: 0.6989 (mmm-85) cc_final: 0.6598 (mmm-85) REVERT: H 216 ILE cc_start: 0.8290 (mp) cc_final: 0.8036 (mt) outliers start: 16 outliers final: 5 residues processed: 176 average time/residue: 0.2038 time to fit residues: 49.0629 Evaluate side-chains 157 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8325 Z= 0.202 Angle : 0.591 10.375 11353 Z= 0.301 Chirality : 0.042 0.150 1329 Planarity : 0.004 0.048 1450 Dihedral : 4.908 59.543 1193 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.41 % Allowed : 14.34 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.05 (0.26), residues: 1103 helix: 0.98 (0.27), residues: 399 sheet: -0.51 (0.31), residues: 253 loop : -0.53 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.018 0.002 PHE H 68 TYR 0.015 0.001 TYR H 190 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 LYS cc_start: 0.8294 (mmmt) cc_final: 0.7859 (mmmt) REVERT: B 259 GLN cc_start: 0.6909 (tp40) cc_final: 0.6644 (mm110) REVERT: C 35 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7633 (mm) REVERT: C 416 TRP cc_start: 0.7784 (m100) cc_final: 0.6940 (m100) REVERT: D 77 ARG cc_start: 0.7080 (mmm-85) cc_final: 0.6627 (mmm-85) REVERT: H 6 GLU cc_start: 0.5877 (mp0) cc_final: 0.5555 (mt-10) REVERT: H 216 ILE cc_start: 0.8246 (mp) cc_final: 0.7914 (mt) outliers start: 19 outliers final: 12 residues processed: 176 average time/residue: 0.2057 time to fit residues: 48.7036 Evaluate side-chains 163 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8325 Z= 0.320 Angle : 0.628 10.099 11353 Z= 0.322 Chirality : 0.044 0.143 1329 Planarity : 0.004 0.043 1450 Dihedral : 5.083 60.905 1193 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.17 % Allowed : 16.62 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.18 (0.26), residues: 1103 helix: 0.91 (0.27), residues: 401 sheet: -0.57 (0.32), residues: 252 loop : -0.67 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.005 0.001 HIS B 225 PHE 0.023 0.002 PHE H 68 TYR 0.019 0.002 TYR H 94 ARG 0.004 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.5994 (p90) REVERT: B 198 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8050 (pp) REVERT: B 259 GLN cc_start: 0.7111 (tp40) cc_final: 0.6811 (mm110) REVERT: C 35 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7608 (mm) REVERT: C 90 TYR cc_start: 0.6115 (m-80) cc_final: 0.5752 (m-80) REVERT: C 416 TRP cc_start: 0.7825 (m100) cc_final: 0.7332 (m100) REVERT: C 421 ILE cc_start: 0.7952 (mm) cc_final: 0.7669 (mt) REVERT: D 77 ARG cc_start: 0.7199 (mmm-85) cc_final: 0.6878 (mmm-85) REVERT: H 6 GLU cc_start: 0.5966 (mp0) cc_final: 0.5602 (mt-10) REVERT: H 216 ILE cc_start: 0.8203 (mp) cc_final: 0.8000 (mt) outliers start: 25 outliers final: 19 residues processed: 177 average time/residue: 0.2058 time to fit residues: 49.2536 Evaluate side-chains 172 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN C 364 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8325 Z= 0.404 Angle : 0.668 10.399 11353 Z= 0.345 Chirality : 0.046 0.231 1329 Planarity : 0.004 0.039 1450 Dihedral : 5.348 62.766 1193 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.44 % Allowed : 16.50 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.51 (0.26), residues: 1103 helix: 0.69 (0.27), residues: 401 sheet: -0.85 (0.31), residues: 251 loop : -0.85 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 169 HIS 0.006 0.001 HIS B 183 PHE 0.026 0.002 PHE H 27 TYR 0.020 0.002 TYR H 94 ARG 0.003 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.6029 (p90) REVERT: B 52 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7684 (mmt90) REVERT: B 114 CYS cc_start: 0.7818 (OUTLIER) cc_final: 0.6938 (m) REVERT: B 169 TRP cc_start: 0.7536 (m100) cc_final: 0.6985 (m100) REVERT: B 198 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8042 (pp) REVERT: B 259 GLN cc_start: 0.7154 (tp40) cc_final: 0.6946 (tp40) REVERT: C 35 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7626 (mm) REVERT: C 90 TYR cc_start: 0.6120 (m-80) cc_final: 0.5797 (m-80) REVERT: C 365 ARG cc_start: 0.8199 (mtp180) cc_final: 0.7967 (mtm-85) REVERT: C 416 TRP cc_start: 0.7965 (m100) cc_final: 0.7558 (m100) REVERT: C 420 CYS cc_start: 0.7493 (m) cc_final: 0.7197 (m) REVERT: C 421 ILE cc_start: 0.8026 (mm) cc_final: 0.7782 (mt) REVERT: D 77 ARG cc_start: 0.7147 (mmm-85) cc_final: 0.6766 (mmm-85) REVERT: H 6 GLU cc_start: 0.6047 (mp0) cc_final: 0.5637 (mt-10) REVERT: H 208 SER cc_start: 0.8528 (t) cc_final: 0.8163 (m) REVERT: H 216 ILE cc_start: 0.8208 (mp) cc_final: 0.7992 (mt) outliers start: 35 outliers final: 22 residues processed: 182 average time/residue: 0.2339 time to fit residues: 57.8200 Evaluate side-chains 178 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8325 Z= 0.236 Angle : 0.587 9.393 11353 Z= 0.302 Chirality : 0.042 0.147 1329 Planarity : 0.004 0.036 1450 Dihedral : 5.025 64.792 1193 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.30 % Allowed : 18.02 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.33 (0.26), residues: 1103 helix: 0.89 (0.27), residues: 400 sheet: -0.83 (0.31), residues: 253 loop : -0.74 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 88 HIS 0.003 0.001 HIS B 225 PHE 0.017 0.002 PHE C 93 TYR 0.016 0.001 TYR H 190 ARG 0.007 0.000 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 TYR cc_start: 0.8155 (m-80) cc_final: 0.7674 (m-80) REVERT: B 169 TRP cc_start: 0.7441 (OUTLIER) cc_final: 0.6906 (m100) REVERT: B 198 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8072 (pp) REVERT: B 259 GLN cc_start: 0.6911 (tp40) cc_final: 0.6631 (mm110) REVERT: C 35 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7619 (mm) REVERT: C 90 TYR cc_start: 0.6069 (m-80) cc_final: 0.5761 (m-80) REVERT: C 365 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7973 (mtm-85) REVERT: C 416 TRP cc_start: 0.7956 (m100) cc_final: 0.7547 (m100) REVERT: C 420 CYS cc_start: 0.7445 (m) cc_final: 0.7191 (m) REVERT: C 421 ILE cc_start: 0.7992 (mm) cc_final: 0.7739 (mt) REVERT: D 77 ARG cc_start: 0.6954 (mmm-85) cc_final: 0.6629 (mmm-85) REVERT: H 6 GLU cc_start: 0.5923 (mp0) cc_final: 0.5483 (mt-10) REVERT: H 208 SER cc_start: 0.8430 (t) cc_final: 0.8043 (m) REVERT: H 216 ILE cc_start: 0.8199 (mp) cc_final: 0.7994 (mt) outliers start: 26 outliers final: 20 residues processed: 174 average time/residue: 0.2014 time to fit residues: 47.6668 Evaluate side-chains 179 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN B 32 GLN C 418 HIS ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8325 Z= 0.240 Angle : 0.588 9.368 11353 Z= 0.304 Chirality : 0.043 0.153 1329 Planarity : 0.004 0.034 1450 Dihedral : 4.906 63.928 1193 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.06 % Allowed : 17.51 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.25 (0.26), residues: 1103 helix: 1.00 (0.27), residues: 400 sheet: -0.80 (0.31), residues: 254 loop : -0.73 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 88 HIS 0.006 0.001 HIS B 225 PHE 0.018 0.002 PHE A 190 TYR 0.016 0.001 TYR H 190 ARG 0.004 0.000 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7034 (OUTLIER) cc_final: 0.6023 (p90) REVERT: B 169 TRP cc_start: 0.7414 (OUTLIER) cc_final: 0.6872 (m100) REVERT: B 198 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8045 (pp) REVERT: B 259 GLN cc_start: 0.6969 (tp40) cc_final: 0.6701 (mm110) REVERT: C 35 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7596 (mm) REVERT: C 90 TYR cc_start: 0.6039 (m-80) cc_final: 0.5823 (m-80) REVERT: C 365 ARG cc_start: 0.8208 (mtp180) cc_final: 0.7890 (mtm-85) REVERT: C 416 TRP cc_start: 0.7924 (m100) cc_final: 0.7533 (m100) REVERT: C 420 CYS cc_start: 0.7449 (m) cc_final: 0.7211 (m) REVERT: C 421 ILE cc_start: 0.7998 (mm) cc_final: 0.7749 (mt) REVERT: D 77 ARG cc_start: 0.6944 (mmm-85) cc_final: 0.6640 (mmm-85) REVERT: H 6 GLU cc_start: 0.5915 (mp0) cc_final: 0.5506 (mt-10) REVERT: H 208 SER cc_start: 0.8418 (t) cc_final: 0.8034 (m) outliers start: 32 outliers final: 22 residues processed: 178 average time/residue: 0.2136 time to fit residues: 52.0872 Evaluate side-chains 177 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8325 Z= 0.230 Angle : 0.585 9.339 11353 Z= 0.301 Chirality : 0.042 0.163 1329 Planarity : 0.004 0.034 1450 Dihedral : 4.805 63.359 1193 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.68 % Allowed : 18.78 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.19 (0.26), residues: 1103 helix: 1.06 (0.27), residues: 398 sheet: -0.70 (0.31), residues: 264 loop : -0.74 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 88 HIS 0.006 0.001 HIS B 225 PHE 0.018 0.002 PHE A 190 TYR 0.015 0.001 TYR H 190 ARG 0.004 0.000 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.5998 (p90) REVERT: B 169 TRP cc_start: 0.7473 (OUTLIER) cc_final: 0.6972 (m100) REVERT: B 198 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8050 (pp) REVERT: B 259 GLN cc_start: 0.6945 (tp40) cc_final: 0.6691 (mm110) REVERT: C 35 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7691 (mm) REVERT: C 90 TYR cc_start: 0.5943 (m-80) cc_final: 0.5717 (m-80) REVERT: C 416 TRP cc_start: 0.7919 (m100) cc_final: 0.7458 (m100) REVERT: C 421 ILE cc_start: 0.7992 (mm) cc_final: 0.7740 (mt) REVERT: D 77 ARG cc_start: 0.6886 (mmm-85) cc_final: 0.6621 (mmm-85) REVERT: H 6 GLU cc_start: 0.5929 (mp0) cc_final: 0.5563 (mt-10) REVERT: H 208 SER cc_start: 0.8386 (t) cc_final: 0.8012 (m) outliers start: 29 outliers final: 22 residues processed: 170 average time/residue: 0.2049 time to fit residues: 47.3344 Evaluate side-chains 175 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 chunk 30 optimal weight: 0.2980 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 0.0050 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 0.3172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8325 Z= 0.165 Angle : 0.564 8.885 11353 Z= 0.288 Chirality : 0.042 0.157 1329 Planarity : 0.004 0.033 1450 Dihedral : 4.593 63.791 1193 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.05 % Allowed : 19.67 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.07 (0.26), residues: 1103 helix: 1.19 (0.27), residues: 396 sheet: -0.66 (0.31), residues: 254 loop : -0.69 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 88 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.001 PHE A 190 TYR 0.013 0.001 TYR H 190 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.6990 (OUTLIER) cc_final: 0.6011 (p90) REVERT: B 169 TRP cc_start: 0.7419 (OUTLIER) cc_final: 0.6947 (m100) REVERT: B 198 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8075 (pp) REVERT: C 35 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7650 (mm) REVERT: C 416 TRP cc_start: 0.7896 (m100) cc_final: 0.7520 (m100) REVERT: C 420 CYS cc_start: 0.7442 (m) cc_final: 0.7221 (m) REVERT: C 421 ILE cc_start: 0.7973 (mm) cc_final: 0.7713 (mt) REVERT: D 77 ARG cc_start: 0.6846 (mmm-85) cc_final: 0.6630 (mmm-85) REVERT: H 38 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.6978 (ttm170) REVERT: H 208 SER cc_start: 0.8311 (t) cc_final: 0.7932 (m) outliers start: 24 outliers final: 17 residues processed: 170 average time/residue: 0.2174 time to fit residues: 49.3775 Evaluate side-chains 173 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8325 Z= 0.264 Angle : 0.611 9.264 11353 Z= 0.314 Chirality : 0.043 0.162 1329 Planarity : 0.004 0.035 1450 Dihedral : 4.722 62.593 1193 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.05 % Allowed : 19.92 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.26), residues: 1103 helix: 1.05 (0.27), residues: 400 sheet: -0.67 (0.30), residues: 270 loop : -0.78 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 88 HIS 0.006 0.001 HIS B 225 PHE 0.020 0.002 PHE A 190 TYR 0.016 0.002 TYR H 190 ARG 0.004 0.000 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6016 (p90) REVERT: B 169 TRP cc_start: 0.7387 (OUTLIER) cc_final: 0.6968 (m100) REVERT: B 198 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8034 (pp) REVERT: C 35 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7622 (mm) REVERT: C 416 TRP cc_start: 0.7937 (m100) cc_final: 0.7556 (m100) REVERT: C 420 CYS cc_start: 0.7476 (m) cc_final: 0.7239 (m) REVERT: C 421 ILE cc_start: 0.8018 (mm) cc_final: 0.7766 (mt) REVERT: D 77 ARG cc_start: 0.6881 (mmm-85) cc_final: 0.6645 (mmm-85) REVERT: H 38 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6355 (ttm170) REVERT: H 208 SER cc_start: 0.8358 (t) cc_final: 0.7981 (m) outliers start: 24 outliers final: 18 residues processed: 166 average time/residue: 0.2006 time to fit residues: 45.4569 Evaluate side-chains 170 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.127607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.110357 restraints weight = 17059.593| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.31 r_work: 0.3695 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8325 Z= 0.194 Angle : 0.581 9.095 11353 Z= 0.298 Chirality : 0.042 0.158 1329 Planarity : 0.004 0.034 1450 Dihedral : 4.633 63.386 1193 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.05 % Allowed : 19.92 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.12 (0.26), residues: 1103 helix: 1.12 (0.27), residues: 400 sheet: -0.60 (0.30), residues: 270 loop : -0.76 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 88 HIS 0.005 0.001 HIS B 225 PHE 0.020 0.001 PHE A 190 TYR 0.014 0.001 TYR H 190 ARG 0.004 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.53 seconds wall clock time: 42 minutes 9.32 seconds (2529.32 seconds total)