Starting phenix.real_space_refine on Mon Mar 11 14:07:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/03_2024/6k41_9911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/03_2024/6k41_9911.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/6k41_9911/03_2024/6k41_9911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/03_2024/6k41_9911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/03_2024/6k41_9911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/03_2024/6k41_9911_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= 0.003 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 55 5.16 5 C 5384 2.51 5 N 1435 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "R ARG 116": "NH1" <-> "NH2" Residue "R ARG 127": "NH1" <-> "NH2" Residue "R ARG 201": "NH1" <-> "NH2" Residue "R PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 439": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8430 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain breaks: 3 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2559 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "R" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1952 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain breaks: 5 Chain: "H" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1793 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CZX': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 3.12, per 1000 atoms: 0.37 Number of scatterers: 8430 At special positions: 0 Unit cell: (109.1, 110.191, 119.464, 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 55 16.00 O 1556 8.00 N 1435 7.00 C 5384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " 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: 3.62 Conformation dependent library (CDL) restraints added in 1.6 seconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 12 sheets defined 33.3% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 7 through 30 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.817A pdb=" N TYR A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 297 through 311 removed outlier: 4.937A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.632A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 24 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.872A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 12 through 38 Processing helix chain 'R' and resid 49 through 73 removed outlier: 3.734A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) Proline residue: R 67 - end of helix Processing helix chain 'R' and resid 86 through 115 Processing helix chain 'R' and resid 117 through 121 Processing helix chain 'R' and resid 126 through 147 Proline residue: R 146 - end of helix Processing helix chain 'R' and resid 171 through 180 removed outlier: 3.630A pdb=" N ALA R 175 " --> pdb=" O TRP R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 202 Processing helix chain 'R' and resid 363 through 392 removed outlier: 3.538A pdb=" N LYS R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE R 380 " --> pdb=" O VAL R 376 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL R 381 " --> pdb=" O ILE R 377 " (cutoff:3.500A) Proline residue: R 386 - end of helix Processing helix chain 'R' and resid 407 through 427 removed outlier: 3.802A pdb=" N TYR R 416 " --> pdb=" O PHE R 412 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN R 418 " --> pdb=" O ILE R 414 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 431 through 441 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.810A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.814A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.785A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.617A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.845A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.549A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.643A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.632A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'H' and resid 115 through 117 removed outlier: 5.824A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 134 through 137 removed outlier: 6.278A pdb=" N LYS H 232 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL H 137 " --> pdb=" O LYS H 232 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU H 234 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY H 213 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE H 177 " --> pdb=" O TRP H 164 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU H 166 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU H 175 " --> pdb=" O LEU H 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 143 through 148 removed outlier: 3.765A pdb=" N ALA H 199 " --> pdb=" O SER H 196 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1086 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: 2.50 Time building geometry restraints manager: 4.04 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: 2170 1.33 - 1.45: 1760 1.45 - 1.57: 4598 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 8603 Sorted by residual: bond pdb=" C09 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.385 1.523 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C11 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.386 1.522 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C08 CZX R 501 " pdb=" C11 CZX R 501 " ideal model delta sigma weight residual 1.392 1.526 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C04 CZX R 501 " pdb=" C09 CZX R 501 " ideal model delta sigma weight residual 1.393 1.521 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C04 CZX R 501 " pdb=" C05 CZX R 501 " ideal model delta sigma weight residual 1.403 1.531 -0.128 2.00e-02 2.50e+03 4.08e+01 ... (remaining 8598 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.55: 193 106.55 - 113.84: 4729 113.84 - 121.13: 4302 121.13 - 128.42: 2351 128.42 - 135.70: 75 Bond angle restraints: 11650 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 113.71 107.35 6.36 9.50e-01 1.11e+00 4.49e+01 angle pdb=" N LEU R 145 " pdb=" CA LEU R 145 " pdb=" C LEU R 145 " ideal model delta sigma weight residual 109.81 122.76 -12.95 2.21e+00 2.05e-01 3.44e+01 angle pdb=" N PRO R 146 " pdb=" CA PRO R 146 " pdb=" C PRO R 146 " ideal model delta sigma weight residual 110.70 116.69 -5.99 1.22e+00 6.72e-01 2.41e+01 angle pdb=" C ARG H 179 " pdb=" N MET H 180 " pdb=" CA MET H 180 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C THR A 296 " pdb=" N TYR A 297 " pdb=" CA TYR A 297 " ideal model delta sigma weight residual 120.54 126.25 -5.71 1.35e+00 5.49e-01 1.79e+01 ... (remaining 11645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 4822 16.48 - 32.95: 219 32.95 - 49.43: 41 49.43 - 65.90: 2 65.90 - 82.38: 6 Dihedral angle restraints: 5090 sinusoidal: 1972 harmonic: 3118 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CA SER B 281 " pdb=" C SER B 281 " pdb=" N GLY B 282 " pdb=" CA GLY B 282 " ideal model delta harmonic sigma weight residual 180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ARG R 116 " pdb=" C ARG R 116 " pdb=" N ALA R 117 " pdb=" CA ALA R 117 " ideal model delta harmonic sigma weight residual -180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 5087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1142 0.087 - 0.174: 169 0.174 - 0.260: 13 0.260 - 0.347: 3 0.347 - 0.434: 1 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CG LEU G 50 " pdb=" CB LEU G 50 " pdb=" CD1 LEU G 50 " pdb=" CD2 LEU G 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB VAL A 219 " pdb=" CA VAL A 219 " pdb=" CG1 VAL A 219 " pdb=" CG2 VAL A 219 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1325 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 62 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ALA R 62 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA R 62 " -0.018 2.00e-02 2.50e+03 pdb=" N THR R 63 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 111 " 0.019 2.00e-02 2.50e+03 1.72e-02 7.43e+00 pdb=" CG TRP H 111 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP H 111 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP H 111 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP H 111 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 111 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 111 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 111 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 50 " -0.019 2.00e-02 2.50e+03 1.94e-02 6.60e+00 pdb=" CG PHE R 50 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE R 50 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE R 50 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE R 50 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE R 50 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE R 50 " -0.001 2.00e-02 2.50e+03 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 302 2.71 - 3.26: 7578 3.26 - 3.81: 13462 3.81 - 4.35: 17801 4.35 - 4.90: 29883 Nonbonded interactions: 69026 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.166 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.189 2.440 nonbonded pdb=" OG SER R 69 " pdb=" OH TYR R 88 " model vdw 2.220 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.243 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR H 163 " model vdw 2.244 2.440 ... (remaining 69021 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 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: 34.380 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 24.200 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.009 0.138 8603 Z= 0.562 Angle : 1.065 15.404 11650 Z= 0.571 Chirality : 0.062 0.434 1328 Planarity : 0.007 0.062 1467 Dihedral : 10.212 74.612 3065 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.44 % Allowed : 3.40 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.22), residues: 1049 helix: -1.40 (0.22), residues: 365 sheet: -0.89 (0.30), residues: 277 loop : -2.54 (0.25), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP H 111 HIS 0.014 0.004 HIS B 62 PHE 0.044 0.004 PHE R 50 TYR 0.030 0.004 TYR B 59 ARG 0.019 0.002 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7554 (m-30) cc_final: 0.7321 (m-30) REVERT: A 193 LYS cc_start: 0.7468 (mtpm) cc_final: 0.7179 (mmpt) REVERT: A 210 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7678 (mmtm) REVERT: A 328 ASP cc_start: 0.7295 (m-30) cc_final: 0.6547 (m-30) REVERT: A 332 ILE cc_start: 0.8282 (mp) cc_final: 0.8001 (mt) REVERT: B 207 SER cc_start: 0.8695 (p) cc_final: 0.8379 (m) REVERT: G 19 LEU cc_start: 0.8030 (mt) cc_final: 0.7745 (mp) REVERT: R 72 ASN cc_start: 0.6408 (t0) cc_final: 0.6057 (t0) REVERT: R 201 ARG cc_start: 0.6969 (ttp-170) cc_final: 0.6739 (tmm160) REVERT: R 407 LEU cc_start: 0.6761 (mt) cc_final: 0.6501 (mm) REVERT: H 3 GLN cc_start: 0.7505 (mt0) cc_final: 0.7304 (mm-40) outliers start: 4 outliers final: 2 residues processed: 212 average time/residue: 1.2988 time to fit residues: 291.0396 Evaluate side-chains 135 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 205 GLN A 214 HIS A 257 ASN B 32 GLN B 239 ASN B 293 ASN R 30 ASN H 167 GLN H 171 GLN H 219 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8603 Z= 0.249 Angle : 0.614 9.938 11650 Z= 0.326 Chirality : 0.045 0.158 1328 Planarity : 0.005 0.048 1467 Dihedral : 5.451 42.212 1173 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.38 % Allowed : 10.62 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: -0.98 (0.25), residues: 1049 helix: 0.66 (0.27), residues: 358 sheet: -0.43 (0.30), residues: 289 loop : -1.99 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.008 0.002 HIS B 62 PHE 0.038 0.002 PHE R 369 TYR 0.025 0.002 TYR B 105 ARG 0.007 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 146 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 193 LYS cc_start: 0.7551 (mtpm) cc_final: 0.7219 (mmpt) REVERT: A 210 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7734 (mmtm) REVERT: A 328 ASP cc_start: 0.7306 (m-30) cc_final: 0.6560 (m-30) REVERT: B 52 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7432 (ptm160) REVERT: B 212 ASP cc_start: 0.7533 (t0) cc_final: 0.7207 (t0) REVERT: B 234 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8239 (t80) REVERT: R 72 ASN cc_start: 0.6521 (t0) cc_final: 0.6250 (t0) REVERT: R 187 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8426 (mm) REVERT: R 201 ARG cc_start: 0.7101 (ttp-170) cc_final: 0.6764 (ttm110) REVERT: R 377 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8162 (tp) REVERT: H 87 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7447 (mtt90) REVERT: H 190 ARG cc_start: 0.6795 (mtm110) cc_final: 0.6507 (mtm110) outliers start: 40 outliers final: 11 residues processed: 167 average time/residue: 1.3336 time to fit residues: 235.5375 Evaluate side-chains 146 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 377 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN H 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8603 Z= 0.201 Angle : 0.555 8.229 11650 Z= 0.294 Chirality : 0.043 0.152 1328 Planarity : 0.004 0.041 1467 Dihedral : 5.047 35.601 1173 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.27 % Allowed : 13.36 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: -0.21 (0.26), residues: 1049 helix: 1.52 (0.28), residues: 350 sheet: -0.10 (0.30), residues: 287 loop : -1.64 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.035 0.002 PHE R 369 TYR 0.014 0.002 TYR B 105 ARG 0.006 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7787 (mtmt) REVERT: A 193 LYS cc_start: 0.7549 (mtpm) cc_final: 0.7247 (mmpt) REVERT: A 210 LYS cc_start: 0.8288 (ttmm) cc_final: 0.7762 (mmtm) REVERT: A 277 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6897 (mm-30) REVERT: A 309 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6900 (mt-10) REVERT: A 328 ASP cc_start: 0.7250 (m-30) cc_final: 0.6373 (m-30) REVERT: B 212 ASP cc_start: 0.7482 (t0) cc_final: 0.7186 (t0) REVERT: R 72 ASN cc_start: 0.6564 (t0) cc_final: 0.6329 (t0) REVERT: R 119 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7458 (tm-30) REVERT: R 187 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8335 (mm) REVERT: R 201 ARG cc_start: 0.7106 (ttp-170) cc_final: 0.6792 (ttm110) REVERT: H 39 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: H 87 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7531 (mtt90) outliers start: 39 outliers final: 20 residues processed: 165 average time/residue: 1.3854 time to fit residues: 241.4188 Evaluate side-chains 157 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 428 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 143 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN H 130 GLN H 167 GLN H 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 8603 Z= 0.218 Angle : 0.558 9.107 11650 Z= 0.293 Chirality : 0.043 0.151 1328 Planarity : 0.004 0.040 1467 Dihedral : 4.971 35.558 1173 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.59 % Allowed : 13.03 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 1049 helix: 1.70 (0.28), residues: 355 sheet: 0.04 (0.30), residues: 287 loop : -1.45 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.033 0.002 PHE R 369 TYR 0.015 0.002 TYR H 59 ARG 0.008 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 132 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8154 (tmmt) REVERT: A 24 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7783 (mtmt) REVERT: A 193 LYS cc_start: 0.7573 (mtpm) cc_final: 0.7270 (mmpt) REVERT: A 210 LYS cc_start: 0.8303 (ttmm) cc_final: 0.7749 (mmtm) REVERT: A 328 ASP cc_start: 0.7229 (m-30) cc_final: 0.6372 (m-30) REVERT: B 212 ASP cc_start: 0.7449 (t0) cc_final: 0.7151 (t0) REVERT: R 72 ASN cc_start: 0.6582 (t0) cc_final: 0.6330 (t0) REVERT: R 127 ARG cc_start: 0.7120 (ptm160) cc_final: 0.6831 (ptt90) REVERT: R 187 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8331 (mm) REVERT: R 201 ARG cc_start: 0.7128 (ttp-170) cc_final: 0.6822 (ttm110) REVERT: R 368 ARG cc_start: 0.6374 (OUTLIER) cc_final: 0.5507 (ttt90) REVERT: H 87 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7558 (mtt90) REVERT: H 166 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8243 (tp) REVERT: H 190 ARG cc_start: 0.6750 (mtm110) cc_final: 0.6544 (mtm110) outliers start: 51 outliers final: 23 residues processed: 164 average time/residue: 1.3323 time to fit residues: 231.5141 Evaluate side-chains 155 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 428 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 166 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 30 ASN H 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8603 Z= 0.303 Angle : 0.636 8.706 11650 Z= 0.332 Chirality : 0.045 0.163 1328 Planarity : 0.005 0.044 1467 Dihedral : 5.354 42.177 1173 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.26 % Allowed : 14.02 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1049 helix: 1.46 (0.27), residues: 356 sheet: 0.03 (0.30), residues: 291 loop : -1.40 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.002 HIS B 62 PHE 0.033 0.002 PHE R 369 TYR 0.014 0.002 TYR R 391 ARG 0.008 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 139 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8020 (tmmt) REVERT: A 24 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7770 (mtmt) REVERT: A 193 LYS cc_start: 0.7686 (mtpm) cc_final: 0.7228 (mmpt) REVERT: A 210 LYS cc_start: 0.8350 (ttmm) cc_final: 0.7741 (mmtm) REVERT: A 323 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7249 (mtm) REVERT: A 328 ASP cc_start: 0.7238 (m-30) cc_final: 0.6347 (m-30) REVERT: B 212 ASP cc_start: 0.7538 (t0) cc_final: 0.7197 (t0) REVERT: R 72 ASN cc_start: 0.6606 (t0) cc_final: 0.6382 (t0) REVERT: R 119 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7603 (tm-30) REVERT: R 187 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8440 (mm) REVERT: R 201 ARG cc_start: 0.7153 (ttp-170) cc_final: 0.6789 (ttm110) REVERT: R 368 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.5700 (ttt90) REVERT: H 39 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: H 87 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7641 (mtt90) REVERT: H 166 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8315 (tp) REVERT: H 174 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8247 (pt0) outliers start: 48 outliers final: 25 residues processed: 171 average time/residue: 1.3491 time to fit residues: 243.6332 Evaluate side-chains 167 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 428 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 174 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 256 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8603 Z= 0.174 Angle : 0.546 10.372 11650 Z= 0.284 Chirality : 0.042 0.148 1328 Planarity : 0.004 0.039 1467 Dihedral : 4.866 35.263 1173 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.26 % Allowed : 14.79 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 1049 helix: 1.82 (0.28), residues: 356 sheet: 0.18 (0.30), residues: 287 loop : -1.38 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.032 0.001 PHE R 369 TYR 0.013 0.001 TYR R 391 ARG 0.008 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 128 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8043 (tmmt) REVERT: A 24 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7783 (mtmt) REVERT: A 54 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.5710 (tppp) REVERT: A 193 LYS cc_start: 0.7652 (mtpm) cc_final: 0.7237 (mmpt) REVERT: A 210 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7748 (mmtm) REVERT: A 323 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7228 (mtm) REVERT: A 328 ASP cc_start: 0.7193 (m-30) cc_final: 0.6372 (m-30) REVERT: B 212 ASP cc_start: 0.7400 (t0) cc_final: 0.7135 (t0) REVERT: R 72 ASN cc_start: 0.6603 (t0) cc_final: 0.6369 (t0) REVERT: R 187 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8299 (mm) REVERT: R 201 ARG cc_start: 0.7152 (ttp-170) cc_final: 0.6807 (ttm110) REVERT: R 368 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5443 (ttt90) REVERT: H 39 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: H 87 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7612 (mtt90) REVERT: H 166 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8272 (tp) REVERT: H 190 ARG cc_start: 0.6792 (mtm110) cc_final: 0.6533 (mtm110) outliers start: 48 outliers final: 27 residues processed: 163 average time/residue: 1.3296 time to fit residues: 229.2185 Evaluate side-chains 162 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain R residue 428 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.1980 chunk 58 optimal weight: 0.0970 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 245 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8603 Z= 0.135 Angle : 0.511 10.334 11650 Z= 0.264 Chirality : 0.041 0.142 1328 Planarity : 0.004 0.039 1467 Dihedral : 4.514 40.177 1173 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.82 % Allowed : 15.77 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.50 (0.26), residues: 1049 helix: 2.13 (0.28), residues: 359 sheet: 0.24 (0.30), residues: 281 loop : -1.27 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.002 0.001 HIS H 35 PHE 0.030 0.001 PHE R 369 TYR 0.014 0.001 TYR H 59 ARG 0.009 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 1.025 Fit side-chains REVERT: A 21 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8178 (tmmt) REVERT: A 24 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7799 (mtmt) REVERT: A 54 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.5671 (tppp) REVERT: A 193 LYS cc_start: 0.7579 (mtpm) cc_final: 0.7286 (mmpt) REVERT: A 210 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7757 (mmtm) REVERT: A 277 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6328 (mp0) REVERT: A 323 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7135 (mtm) REVERT: A 328 ASP cc_start: 0.7148 (m-30) cc_final: 0.6296 (m-30) REVERT: B 212 ASP cc_start: 0.7281 (t0) cc_final: 0.6502 (t0) REVERT: B 217 MET cc_start: 0.8088 (pmm) cc_final: 0.7622 (pmm) REVERT: B 219 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6450 (mpt-90) REVERT: R 72 ASN cc_start: 0.6625 (t0) cc_final: 0.6371 (t0) REVERT: R 127 ARG cc_start: 0.7093 (ptm160) cc_final: 0.6779 (ptt90) REVERT: R 187 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8205 (mt) REVERT: R 201 ARG cc_start: 0.7144 (ttp-170) cc_final: 0.6806 (ttm110) REVERT: R 368 ARG cc_start: 0.6334 (OUTLIER) cc_final: 0.5383 (ttt90) REVERT: H 39 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: H 87 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7601 (mtt90) REVERT: H 166 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8206 (tp) REVERT: H 212 VAL cc_start: 0.7330 (t) cc_final: 0.6961 (p) outliers start: 44 outliers final: 21 residues processed: 168 average time/residue: 1.3138 time to fit residues: 233.5188 Evaluate side-chains 158 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain R residue 428 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 0.4980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 233 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 239 ASN B 340 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8603 Z= 0.333 Angle : 0.657 10.408 11650 Z= 0.340 Chirality : 0.047 0.167 1328 Planarity : 0.005 0.045 1467 Dihedral : 5.195 42.648 1172 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.82 % Allowed : 15.12 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1049 helix: 1.70 (0.27), residues: 356 sheet: 0.18 (0.30), residues: 291 loop : -1.29 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.002 HIS B 54 PHE 0.032 0.002 PHE R 369 TYR 0.015 0.002 TYR R 391 ARG 0.010 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8024 (tmmt) REVERT: A 24 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7769 (mtmt) REVERT: A 54 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.5726 (tppp) REVERT: A 193 LYS cc_start: 0.7681 (mtpm) cc_final: 0.7270 (mmpt) REVERT: A 210 LYS cc_start: 0.8338 (ttmm) cc_final: 0.7738 (mmtm) REVERT: A 323 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7196 (mtm) REVERT: A 328 ASP cc_start: 0.7216 (m-30) cc_final: 0.6373 (m-30) REVERT: B 212 ASP cc_start: 0.7479 (t0) cc_final: 0.7206 (t0) REVERT: R 72 ASN cc_start: 0.6628 (t0) cc_final: 0.6404 (t0) REVERT: R 187 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8471 (mm) REVERT: R 201 ARG cc_start: 0.7189 (ttp-170) cc_final: 0.6840 (ttm110) REVERT: R 368 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5679 (ttt90) REVERT: R 377 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8354 (tp) REVERT: H 87 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7652 (mtt90) REVERT: H 166 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8329 (tp) outliers start: 44 outliers final: 22 residues processed: 161 average time/residue: 1.3660 time to fit residues: 232.6224 Evaluate side-chains 162 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain R residue 377 ILE Chi-restraints excluded: chain R residue 428 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 41 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 0.0050 chunk 100 optimal weight: 0.0570 overall best weight: 0.2512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 233 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8603 Z= 0.121 Angle : 0.501 10.564 11650 Z= 0.259 Chirality : 0.040 0.138 1328 Planarity : 0.004 0.043 1467 Dihedral : 4.391 42.484 1172 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.96 % Allowed : 17.52 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.62 (0.26), residues: 1049 helix: 2.21 (0.28), residues: 359 sheet: 0.37 (0.30), residues: 285 loop : -1.25 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 297 HIS 0.002 0.001 HIS H 35 PHE 0.030 0.001 PHE R 369 TYR 0.011 0.001 TYR B 105 ARG 0.010 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 0.997 Fit side-chains REVERT: A 24 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7796 (mtmt) REVERT: A 54 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.5640 (tppp) REVERT: A 193 LYS cc_start: 0.7594 (mtpm) cc_final: 0.7292 (mmpt) REVERT: A 210 LYS cc_start: 0.8295 (ttmm) cc_final: 0.7750 (mmtm) REVERT: A 328 ASP cc_start: 0.7160 (m-30) cc_final: 0.6262 (m-30) REVERT: B 46 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7201 (ttm110) REVERT: B 212 ASP cc_start: 0.7259 (t0) cc_final: 0.6560 (t0) REVERT: B 219 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6467 (mpt-90) REVERT: B 234 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7784 (t80) REVERT: B 262 MET cc_start: 0.8086 (ttm) cc_final: 0.7878 (ttm) REVERT: G 37 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7473 (tp) REVERT: R 72 ASN cc_start: 0.6629 (t0) cc_final: 0.6351 (t0) REVERT: R 127 ARG cc_start: 0.7010 (ptm160) cc_final: 0.6563 (ptt90) REVERT: R 187 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8161 (mt) REVERT: R 201 ARG cc_start: 0.7137 (ttp-170) cc_final: 0.6817 (ttm110) REVERT: R 368 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.5374 (ttt90) REVERT: H 212 VAL cc_start: 0.7318 (t) cc_final: 0.7008 (p) outliers start: 27 outliers final: 14 residues processed: 154 average time/residue: 1.3514 time to fit residues: 220.0564 Evaluate side-chains 155 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain R residue 428 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 8 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 233 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8603 Z= 0.163 Angle : 0.530 10.276 11650 Z= 0.273 Chirality : 0.042 0.146 1328 Planarity : 0.004 0.047 1467 Dihedral : 4.495 40.051 1172 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.18 % Allowed : 18.40 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.67 (0.26), residues: 1049 helix: 2.28 (0.28), residues: 356 sheet: 0.40 (0.30), residues: 287 loop : -1.23 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.030 0.001 PHE R 369 TYR 0.013 0.001 TYR H 59 ARG 0.011 0.001 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.019 Fit side-chains REVERT: A 24 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7820 (mtmt) REVERT: A 54 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.5653 (tppp) REVERT: A 193 LYS cc_start: 0.7593 (mtpm) cc_final: 0.7291 (mmpt) REVERT: A 210 LYS cc_start: 0.8311 (ttmm) cc_final: 0.7777 (mmtm) REVERT: A 328 ASP cc_start: 0.7147 (m-30) cc_final: 0.6333 (m-30) REVERT: B 212 ASP cc_start: 0.7269 (t0) cc_final: 0.6525 (t0) REVERT: B 214 ARG cc_start: 0.7296 (mmt90) cc_final: 0.6986 (mmt90) REVERT: B 219 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6414 (mpt-90) REVERT: R 72 ASN cc_start: 0.6702 (t0) cc_final: 0.6431 (t0) REVERT: R 127 ARG cc_start: 0.7153 (ptm160) cc_final: 0.6679 (ptt90) REVERT: R 187 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8243 (mt) REVERT: R 201 ARG cc_start: 0.7155 (ttp-170) cc_final: 0.6832 (ttm110) REVERT: R 368 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.5888 (ttt90) REVERT: H 88 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7979 (m) outliers start: 29 outliers final: 19 residues processed: 149 average time/residue: 1.4738 time to fit residues: 231.9239 Evaluate side-chains 149 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 368 ARG Chi-restraints excluded: chain R residue 428 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.162746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.152297 restraints weight = 8803.320| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 0.68 r_work: 0.3470 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8603 Z= 0.138 Angle : 0.511 10.255 11650 Z= 0.263 Chirality : 0.041 0.142 1328 Planarity : 0.004 0.046 1467 Dihedral : 4.374 41.892 1172 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.07 % Allowed : 18.51 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.79 (0.26), residues: 1049 helix: 2.40 (0.28), residues: 357 sheet: 0.47 (0.30), residues: 279 loop : -1.16 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.002 0.001 HIS B 142 PHE 0.030 0.001 PHE R 369 TYR 0.011 0.001 TYR R 391 ARG 0.011 0.001 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4358.07 seconds wall clock time: 78 minutes 10.57 seconds (4690.57 seconds total)