Starting phenix.real_space_refine (version: dev) on Mon Dec 12 01:04:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/12_2022/6k41_9911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/12_2022/6k41_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_9911/12_2022/6k41_9911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/12_2022/6k41_9911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/12_2022/6k41_9911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/12_2022/6k41_9911_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Convert atoms to be neutral 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 4.85, per 1000 atoms: 0.58 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: 3.02 Conformation dependent library (CDL) restraints added in 1.3 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: 0.85 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: 2.49 Time building geometry restraints manager: 3.24 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: 4818 16.48 - 32.95: 215 32.95 - 49.43: 41 49.43 - 65.90: 2 65.90 - 82.38: 6 Dihedral angle restraints: 5082 sinusoidal: 1964 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 5079 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 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: 13.270 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 25.850 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 10.196 74.612 3057 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 0.44 % 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 *********************** 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 : 0.902 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 212 average time/residue: 1.2245 time to fit residues: 275.5730 Evaluate side-chains 134 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.3847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 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: 1.2984 ------------------------------------------------------------------------------- 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: 0.8531 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8603 Z= 0.244 Angle : 0.628 10.170 11650 Z= 0.331 Chirality : 0.045 0.161 1328 Planarity : 0.005 0.049 1467 Dihedral : 5.195 22.966 1162 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 4.49 % 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: -1.04 (0.25), residues: 1049 helix: 0.62 (0.27), residues: 358 sheet: -0.46 (0.30), residues: 289 loop : -2.05 (0.27), residues: 402 *********************** 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 184 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 11 residues processed: 165 average time/residue: 1.3037 time to fit residues: 228.1710 Evaluate side-chains 140 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 1.0221 time to fit residues: 6.8917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 0.0570 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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 R 30 ASN H 167 GLN H 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2756 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= 0.167 Angle : 0.537 8.018 11650 Z= 0.283 Chirality : 0.042 0.149 1328 Planarity : 0.004 0.042 1467 Dihedral : 4.643 22.457 1162 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 3.83 % 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: -0.20 (0.26), residues: 1049 helix: 1.56 (0.28), residues: 352 sheet: -0.13 (0.30), residues: 287 loop : -1.65 (0.28), residues: 410 *********************** 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 165 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 149 average time/residue: 1.3490 time to fit residues: 212.9332 Evaluate side-chains 143 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 6 average time/residue: 0.8765 time to fit residues: 7.0774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.0010 chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 155 ASN R 30 ASN R 72 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.094 8603 Z= 0.159 Angle : 0.501 7.300 11650 Z= 0.265 Chirality : 0.041 0.142 1328 Planarity : 0.004 0.039 1467 Dihedral : 4.326 22.276 1162 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 4.16 % 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: 0.19 (0.26), residues: 1049 helix: 1.95 (0.28), residues: 355 sheet: 0.09 (0.30), residues: 281 loop : -1.51 (0.28), residues: 413 *********************** 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 174 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.006 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 158 average time/residue: 1.1961 time to fit residues: 201.3675 Evaluate side-chains 144 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.6892 time to fit residues: 5.1759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 155 ASN R 30 ASN R 72 ASN H 130 GLN H 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 8603 Z= 0.257 Angle : 0.596 8.346 11650 Z= 0.314 Chirality : 0.045 0.157 1328 Planarity : 0.004 0.043 1467 Dihedral : 4.808 22.464 1162 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 5.04 % 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: 0.18 (0.26), residues: 1049 helix: 1.76 (0.27), residues: 355 sheet: 0.12 (0.30), residues: 289 loop : -1.38 (0.29), residues: 405 *********************** 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 185 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 139 time to evaluate : 1.021 Fit side-chains outliers start: 46 outliers final: 18 residues processed: 166 average time/residue: 1.3377 time to fit residues: 235.4647 Evaluate side-chains 154 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.1124 time to fit residues: 1.8686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 155 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN H 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8603 Z= 0.184 Angle : 0.554 9.168 11650 Z= 0.287 Chirality : 0.042 0.148 1328 Planarity : 0.004 0.045 1467 Dihedral : 4.554 22.719 1162 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 4.05 % 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: 0.35 (0.26), residues: 1049 helix: 1.92 (0.28), residues: 356 sheet: 0.20 (0.30), residues: 293 loop : -1.31 (0.30), residues: 400 *********************** 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 170 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 133 time to evaluate : 1.068 Fit side-chains outliers start: 37 outliers final: 21 residues processed: 159 average time/residue: 1.2645 time to fit residues: 213.4541 Evaluate side-chains 151 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.1244 time to fit residues: 2.1236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 0.0170 chunk 74 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 102 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 155 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN H 82 GLN H 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8603 Z= 0.128 Angle : 0.504 9.320 11650 Z= 0.261 Chirality : 0.041 0.140 1328 Planarity : 0.004 0.044 1467 Dihedral : 4.143 22.324 1162 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 3.72 % 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: 0.60 (0.26), residues: 1049 helix: 2.25 (0.28), residues: 357 sheet: 0.28 (0.30), residues: 281 loop : -1.22 (0.29), residues: 411 *********************** 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 174 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 0.962 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 163 average time/residue: 1.2082 time to fit residues: 209.3061 Evaluate side-chains 149 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.9661 time to fit residues: 5.4602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 72 ASN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8603 Z= 0.166 Angle : 0.534 9.698 11650 Z= 0.277 Chirality : 0.042 0.146 1328 Planarity : 0.004 0.059 1467 Dihedral : 4.331 21.929 1162 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 3.18 % 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: 0.60 (0.26), residues: 1049 helix: 2.25 (0.28), residues: 356 sheet: 0.29 (0.30), residues: 289 loop : -1.23 (0.30), residues: 404 *********************** 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 155 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.045 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 145 average time/residue: 1.2915 time to fit residues: 198.5929 Evaluate side-chains 146 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.4072 time to fit residues: 3.1229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8603 Z= 0.172 Angle : 0.543 10.115 11650 Z= 0.280 Chirality : 0.042 0.146 1328 Planarity : 0.004 0.048 1467 Dihedral : 4.328 21.954 1162 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 3.18 % 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: 0.65 (0.26), residues: 1049 helix: 2.28 (0.28), residues: 356 sheet: 0.40 (0.30), residues: 281 loop : -1.25 (0.29), residues: 412 *********************** 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 157 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.033 Fit side-chains outliers start: 29 outliers final: 22 residues processed: 149 average time/residue: 1.3221 time to fit residues: 209.3579 Evaluate side-chains 146 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.8018 time to fit residues: 4.8248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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** G 44 HIS ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8603 Z= 0.260 Angle : 0.605 10.570 11650 Z= 0.313 Chirality : 0.044 0.157 1328 Planarity : 0.005 0.051 1467 Dihedral : 4.691 22.223 1162 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 3.07 % 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: 0.50 (0.26), residues: 1049 helix: 2.03 (0.27), residues: 356 sheet: 0.32 (0.29), residues: 300 loop : -1.27 (0.30), residues: 393 ********************** 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 159 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 0.947 Fit side-chains outliers start: 28 outliers final: 20 residues processed: 152 average time/residue: 1.2877 time to fit residues: 207.6246 Evaluate side-chains 147 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.5765 time to fit residues: 2.5626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** R 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.160893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.151239 restraints weight = 8779.513| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 0.69 r_work: 0.3460 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8603 Z= 0.165 Angle : 0.548 10.939 11650 Z= 0.282 Chirality : 0.042 0.147 1328 Planarity : 0.004 0.052 1467 Dihedral : 4.415 22.065 1162 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 2.63 % 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: 0.64 (0.26), residues: 1049 helix: 2.24 (0.28), residues: 356 sheet: 0.43 (0.29), residues: 290 loop : -1.28 (0.29), residues: 403 =============================================================================== Job complete usr+sys time: 3921.98 seconds wall clock time: 70 minutes 1.23 seconds (4201.23 seconds total)