Starting phenix.real_space_refine on Fri Jul 19 14:42:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/07_2024/8w89_37349.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/07_2024/8w89_37349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/07_2024/8w89_37349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/07_2024/8w89_37349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/07_2024/8w89_37349.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/07_2024/8w89_37349.cif" } resolution = 3.0 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= 0.026 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 61 5.16 5 C 5229 2.51 5 N 1419 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 61": "NH1" <-> "NH2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 169": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8230 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1934 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2283 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PEA': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.96, per 1000 atoms: 0.60 Number of scatterers: 8230 At special positions: 0 Unit cell: (81.536, 100.672, 132.288, 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 61 16.00 O 1521 8.00 N 1419 7.00 C 5229 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " 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: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 42.5% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 12 through 35 Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.724A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.735A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.188A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 183 through 204 removed outlier: 3.650A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.617A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 52 removed outlier: 4.354A pdb=" N LYS R 52 " --> pdb=" O ILE R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 76 removed outlier: 3.607A pdb=" N LEU R 61 " --> pdb=" O PRO R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 85 Processing helix chain 'R' and resid 92 through 127 Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 231 Processing helix chain 'R' and resid 247 through 274 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 275 through 279 removed outlier: 4.137A pdb=" N HIS R 278 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR R 279 " --> pdb=" O PHE R 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 275 through 279' Processing helix chain 'R' and resid 282 through 306 removed outlier: 3.612A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP R 291 " --> pdb=" O ASP R 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 316 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75 removed outlier: 3.632A pdb=" N PHE A 70 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL A 86 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU A 45 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.784A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.699A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.886A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.651A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.881A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.507A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.518A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.503A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.548A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1233 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: 2.30 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1806 1.33 - 1.46: 2217 1.46 - 1.58: 4297 1.58 - 1.71: 0 1.71 - 1.84: 88 Bond restraints: 8408 Sorted by residual: bond pdb=" CA TYR R 122 " pdb=" C TYR R 122 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.27e-02 6.20e+03 1.75e+01 bond pdb=" CA ARG N 98 " pdb=" C ARG N 98 " ideal model delta sigma weight residual 1.526 1.474 0.052 1.37e-02 5.33e+03 1.43e+01 bond pdb=" CA THR A 216 " pdb=" C THR A 216 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.21e-02 6.83e+03 1.18e+01 bond pdb=" CA TRP B 297 " pdb=" C TRP B 297 " ideal model delta sigma weight residual 1.523 1.485 0.039 1.18e-02 7.18e+03 1.07e+01 bond pdb=" CA ASN R 296 " pdb=" C ASN R 296 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.02e+01 ... (remaining 8403 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.98: 221 106.98 - 113.80: 4620 113.80 - 120.62: 3572 120.62 - 127.44: 2886 127.44 - 134.25: 89 Bond angle restraints: 11388 Sorted by residual: angle pdb=" N GLN R 53 " pdb=" CA GLN R 53 " pdb=" C GLN R 53 " ideal model delta sigma weight residual 113.38 104.99 8.39 1.23e+00 6.61e-01 4.65e+01 angle pdb=" N HIS R 50 " pdb=" CA HIS R 50 " pdb=" C HIS R 50 " ideal model delta sigma weight residual 111.36 118.67 -7.31 1.09e+00 8.42e-01 4.50e+01 angle pdb=" N ARG R 23 " pdb=" CA ARG R 23 " pdb=" C ARG R 23 " ideal model delta sigma weight residual 111.28 104.39 6.89 1.09e+00 8.42e-01 3.99e+01 angle pdb=" N GLN B 259 " pdb=" CA GLN B 259 " pdb=" C GLN B 259 " ideal model delta sigma weight residual 109.14 117.78 -8.64 1.49e+00 4.50e-01 3.36e+01 angle pdb=" N ASP B 228 " pdb=" CA ASP B 228 " pdb=" C ASP B 228 " ideal model delta sigma weight residual 110.24 117.28 -7.04 1.47e+00 4.63e-01 2.29e+01 ... (remaining 11383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4545 17.55 - 35.10: 367 35.10 - 52.65: 68 52.65 - 70.20: 12 70.20 - 87.75: 5 Dihedral angle restraints: 4997 sinusoidal: 1957 harmonic: 3040 Sorted by residual: dihedral pdb=" N ASP B 258 " pdb=" C ASP B 258 " pdb=" CA ASP B 258 " pdb=" CB ASP B 258 " ideal model delta harmonic sigma weight residual 122.80 132.20 -9.40 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 62.27 30.73 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" C VAL R 288 " pdb=" N VAL R 288 " pdb=" CA VAL R 288 " pdb=" CB VAL R 288 " ideal model delta harmonic sigma weight residual -122.00 -130.56 8.56 0 2.50e+00 1.60e-01 1.17e+01 ... (remaining 4994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1083 0.076 - 0.152: 146 0.152 - 0.229: 29 0.229 - 0.305: 11 0.305 - 0.381: 3 Chirality restraints: 1272 Sorted by residual: chirality pdb=" CA ASP B 258 " pdb=" N ASP B 258 " pdb=" C ASP B 258 " pdb=" CB ASP B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA PHE R 268 " pdb=" N PHE R 268 " pdb=" C PHE R 268 " pdb=" CB PHE R 268 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA TRP A 96 " pdb=" N TRP A 96 " pdb=" C TRP A 96 " pdb=" CB TRP A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 1269 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 94 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C VAL R 94 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL R 94 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE R 95 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 48 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C ILE R 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ILE R 48 " -0.019 2.00e-02 2.50e+03 pdb=" N SER R 49 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS R 265 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO R 266 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO R 266 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 266 " 0.039 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2856 2.85 - 3.36: 7727 3.36 - 3.87: 13913 3.87 - 4.39: 16285 4.39 - 4.90: 28042 Nonbonded interactions: 68823 Sorted by model distance: nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.334 2.440 nonbonded pdb=" OG1 THR R 37 " pdb=" OG1 THR R 298 " model vdw 2.368 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.382 2.440 nonbonded pdb=" O SER R 115 " pdb=" OG SER R 118 " model vdw 2.407 2.440 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.430 2.520 ... (remaining 68818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.190 Find NCS groups from input model: 0.060 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.006 0.053 8408 Z= 0.395 Angle : 0.826 10.489 11388 Z= 0.525 Chirality : 0.063 0.381 1272 Planarity : 0.005 0.067 1452 Dihedral : 13.331 87.748 3024 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.90 % Allowed : 2.24 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1031 helix: 2.05 (0.26), residues: 392 sheet: 0.11 (0.36), residues: 216 loop : -0.58 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 96 HIS 0.002 0.001 HIS R 63 PHE 0.023 0.002 PHE B 235 TYR 0.021 0.001 TYR A 210 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 0.912 Fit side-chains REVERT: B 34 THR cc_start: 0.8595 (p) cc_final: 0.8055 (p) REVERT: B 175 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7335 (mp10) REVERT: G 21 MET cc_start: 0.7482 (mtm) cc_final: 0.7240 (mmt) REVERT: R 182 CYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4802 (p) outliers start: 8 outliers final: 0 residues processed: 163 average time/residue: 1.1711 time to fit residues: 203.1728 Evaluate side-chains 131 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.0370 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 223 ASN B 88 ASN B 220 GLN B 259 GLN R 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8408 Z= 0.174 Angle : 0.529 6.586 11388 Z= 0.282 Chirality : 0.042 0.320 1272 Planarity : 0.004 0.045 1452 Dihedral : 4.472 59.690 1142 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.23 % Allowed : 12.23 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1031 helix: 2.33 (0.26), residues: 396 sheet: 0.20 (0.35), residues: 201 loop : -0.54 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 64 PHE 0.017 0.001 PHE A 70 TYR 0.016 0.001 TYR A 210 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: B 34 THR cc_start: 0.8631 (p) cc_final: 0.8180 (p) REVERT: B 101 MET cc_start: 0.8403 (mtp) cc_final: 0.8171 (mtp) REVERT: B 175 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7436 (mp10) REVERT: B 264 TYR cc_start: 0.8464 (m-80) cc_final: 0.8226 (m-80) REVERT: B 293 ASN cc_start: 0.7697 (m-40) cc_final: 0.7394 (p0) REVERT: N 3 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: N 12 VAL cc_start: 0.8523 (p) cc_final: 0.8271 (m) REVERT: R 143 MET cc_start: 0.8035 (mtt) cc_final: 0.7689 (mtm) REVERT: R 166 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7635 (mptp) REVERT: R 182 CYS cc_start: 0.5779 (OUTLIER) cc_final: 0.5097 (p) outliers start: 11 outliers final: 4 residues processed: 147 average time/residue: 1.1060 time to fit residues: 173.8415 Evaluate side-chains 133 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.0060 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 88 ASN B 259 GLN B 340 ASN R 175 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8408 Z= 0.178 Angle : 0.512 6.629 11388 Z= 0.271 Chirality : 0.042 0.311 1272 Planarity : 0.004 0.039 1452 Dihedral : 4.467 58.321 1142 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.24 % Allowed : 14.37 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1031 helix: 2.25 (0.25), residues: 396 sheet: 0.21 (0.35), residues: 197 loop : -0.57 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS A 209 PHE 0.040 0.001 PHE A 70 TYR 0.023 0.001 TYR R 172 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: B 101 MET cc_start: 0.8424 (mtp) cc_final: 0.8135 (mtp) REVERT: B 175 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7395 (mp10) REVERT: B 269 ILE cc_start: 0.8515 (mm) cc_final: 0.8150 (mm) REVERT: B 293 ASN cc_start: 0.7700 (m-40) cc_final: 0.7449 (p0) REVERT: G 42 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: N 12 VAL cc_start: 0.8496 (p) cc_final: 0.8209 (m) REVERT: R 77 MET cc_start: 0.8634 (mtm) cc_final: 0.8396 (mtt) REVERT: R 143 MET cc_start: 0.8068 (mtt) cc_final: 0.7768 (mtm) REVERT: R 158 MET cc_start: 0.7138 (ttm) cc_final: 0.6521 (ttm) REVERT: R 166 LYS cc_start: 0.7545 (mmtt) cc_final: 0.7299 (mptp) outliers start: 20 outliers final: 5 residues processed: 146 average time/residue: 1.0926 time to fit residues: 170.8187 Evaluate side-chains 132 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 131 ASN A 144 ASN A 146 GLN B 75 GLN B 88 ASN B 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8408 Z= 0.167 Angle : 0.506 8.257 11388 Z= 0.266 Chirality : 0.042 0.357 1272 Planarity : 0.003 0.037 1452 Dihedral : 4.416 58.876 1142 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.24 % Allowed : 15.82 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1031 helix: 2.25 (0.26), residues: 396 sheet: 0.29 (0.35), residues: 189 loop : -0.52 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 209 PHE 0.041 0.001 PHE A 70 TYR 0.022 0.001 TYR R 172 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 157 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7602 (mtpt) REVERT: B 34 THR cc_start: 0.8085 (p) cc_final: 0.7618 (t) REVERT: B 101 MET cc_start: 0.8424 (mtp) cc_final: 0.8155 (mtp) REVERT: B 175 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7418 (mp10) REVERT: B 262 MET cc_start: 0.7649 (tpp) cc_final: 0.7289 (mmt) REVERT: G 17 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7166 (pp20) REVERT: N 12 VAL cc_start: 0.8486 (p) cc_final: 0.8200 (m) REVERT: R 52 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7323 (mtmp) REVERT: R 143 MET cc_start: 0.8047 (mtt) cc_final: 0.7739 (mtm) REVERT: R 166 LYS cc_start: 0.7409 (mmtt) cc_final: 0.7141 (mptp) outliers start: 20 outliers final: 6 residues processed: 143 average time/residue: 1.1790 time to fit residues: 179.5905 Evaluate side-chains 138 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 52 LYS Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 146 GLN B 88 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8408 Z= 0.198 Angle : 0.517 6.872 11388 Z= 0.275 Chirality : 0.041 0.189 1272 Planarity : 0.003 0.036 1452 Dihedral : 4.432 57.133 1142 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.81 % Allowed : 16.95 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1031 helix: 2.14 (0.26), residues: 399 sheet: 0.34 (0.36), residues: 170 loop : -0.55 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS A 82 PHE 0.044 0.002 PHE A 70 TYR 0.018 0.001 TYR R 172 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: B 34 THR cc_start: 0.7985 (p) cc_final: 0.7527 (t) REVERT: B 269 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8103 (mm) REVERT: G 17 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7244 (pp20) REVERT: G 42 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: N 3 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: N 12 VAL cc_start: 0.8523 (p) cc_final: 0.8230 (m) REVERT: N 76 LYS cc_start: 0.8587 (mptt) cc_final: 0.8255 (mptt) REVERT: R 52 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7330 (mtmp) REVERT: R 158 MET cc_start: 0.7126 (ttm) cc_final: 0.6496 (ttm) REVERT: R 166 LYS cc_start: 0.7325 (mmtt) cc_final: 0.7092 (mptp) outliers start: 25 outliers final: 7 residues processed: 147 average time/residue: 1.1632 time to fit residues: 181.9551 Evaluate side-chains 137 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain R residue 52 LYS Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.8980 chunk 19 optimal weight: 0.0670 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 0.0570 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN B 88 ASN B 119 ASN B 259 GLN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8408 Z= 0.143 Angle : 0.507 12.016 11388 Z= 0.267 Chirality : 0.042 0.421 1272 Planarity : 0.003 0.037 1452 Dihedral : 4.289 56.344 1142 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.80 % Allowed : 18.63 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1031 helix: 2.18 (0.26), residues: 396 sheet: 0.41 (0.36), residues: 167 loop : -0.52 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 87 PHE 0.037 0.001 PHE A 70 TYR 0.017 0.001 TYR R 172 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8419 (t0) cc_final: 0.8092 (m110) REVERT: B 34 THR cc_start: 0.7796 (p) cc_final: 0.7393 (t) REVERT: B 101 MET cc_start: 0.8365 (mtp) cc_final: 0.8153 (mtp) REVERT: G 17 GLU cc_start: 0.7585 (pt0) cc_final: 0.7228 (pp20) REVERT: G 42 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: N 12 VAL cc_start: 0.8469 (p) cc_final: 0.8174 (m) REVERT: R 52 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7175 (mtmp) REVERT: R 143 MET cc_start: 0.8027 (mtt) cc_final: 0.7758 (mtm) REVERT: R 158 MET cc_start: 0.6926 (ttm) cc_final: 0.6347 (ttm) outliers start: 16 outliers final: 6 residues processed: 146 average time/residue: 1.1146 time to fit residues: 173.6843 Evaluate side-chains 133 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 52 LYS Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 0.0370 chunk 38 optimal weight: 0.1980 chunk 58 optimal weight: 5.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 144 ASN A 146 GLN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8408 Z= 0.155 Angle : 0.517 11.416 11388 Z= 0.271 Chirality : 0.042 0.371 1272 Planarity : 0.003 0.039 1452 Dihedral : 4.226 55.175 1142 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.57 % Allowed : 19.53 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1031 helix: 2.14 (0.26), residues: 398 sheet: 0.49 (0.36), residues: 170 loop : -0.47 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 310 HIS 0.003 0.001 HIS A 209 PHE 0.044 0.001 PHE A 70 TYR 0.014 0.001 TYR R 172 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8416 (t0) cc_final: 0.8087 (m110) REVERT: A 157 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7582 (mtpt) REVERT: B 34 THR cc_start: 0.7717 (p) cc_final: 0.7321 (t) REVERT: B 101 MET cc_start: 0.8400 (mtp) cc_final: 0.8178 (mtp) REVERT: B 234 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8726 (m-80) REVERT: G 17 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7233 (pp20) REVERT: G 42 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: N 3 GLN cc_start: 0.7841 (pt0) cc_final: 0.7438 (tt0) REVERT: N 12 VAL cc_start: 0.8482 (p) cc_final: 0.8193 (m) REVERT: R 52 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7141 (mtmp) REVERT: R 143 MET cc_start: 0.8057 (mtt) cc_final: 0.7764 (mtm) outliers start: 14 outliers final: 6 residues processed: 132 average time/residue: 1.2124 time to fit residues: 170.5428 Evaluate side-chains 133 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 52 LYS Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.2980 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8408 Z= 0.174 Angle : 0.529 13.184 11388 Z= 0.277 Chirality : 0.042 0.423 1272 Planarity : 0.003 0.041 1452 Dihedral : 4.237 53.005 1142 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.57 % Allowed : 20.20 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1031 helix: 2.11 (0.26), residues: 396 sheet: 0.44 (0.36), residues: 172 loop : -0.48 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 310 HIS 0.003 0.001 HIS R 63 PHE 0.041 0.001 PHE A 70 TYR 0.013 0.001 TYR A 191 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8423 (t0) cc_final: 0.8093 (m110) REVERT: A 157 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7614 (mtpt) REVERT: B 34 THR cc_start: 0.7590 (p) cc_final: 0.7195 (t) REVERT: B 101 MET cc_start: 0.8498 (mtp) cc_final: 0.8187 (mtp) REVERT: B 234 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8829 (m-80) REVERT: G 17 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7251 (pp20) REVERT: G 42 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: N 3 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: N 12 VAL cc_start: 0.8484 (p) cc_final: 0.8186 (m) REVERT: R 52 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7128 (mtmp) REVERT: R 153 VAL cc_start: 0.8453 (t) cc_final: 0.8221 (m) outliers start: 14 outliers final: 7 residues processed: 134 average time/residue: 1.1651 time to fit residues: 166.2425 Evaluate side-chains 135 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 52 LYS Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8408 Z= 0.200 Angle : 0.540 11.861 11388 Z= 0.284 Chirality : 0.043 0.411 1272 Planarity : 0.003 0.042 1452 Dihedral : 4.312 49.993 1142 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.68 % Allowed : 20.09 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1031 helix: 2.10 (0.26), residues: 399 sheet: 0.37 (0.36), residues: 173 loop : -0.54 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 310 HIS 0.003 0.001 HIS A 209 PHE 0.040 0.002 PHE A 70 TYR 0.016 0.001 TYR A 210 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8436 (t0) cc_final: 0.8102 (m110) REVERT: B 101 MET cc_start: 0.8532 (mtp) cc_final: 0.8213 (mtp) REVERT: B 234 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8875 (m-80) REVERT: G 17 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7226 (pp20) REVERT: G 42 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: N 3 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: N 12 VAL cc_start: 0.8497 (p) cc_final: 0.8195 (m) REVERT: R 153 VAL cc_start: 0.8485 (t) cc_final: 0.8241 (m) outliers start: 15 outliers final: 8 residues processed: 137 average time/residue: 1.2046 time to fit residues: 175.9136 Evaluate side-chains 133 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN B 75 GLN B 88 ASN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8408 Z= 0.200 Angle : 0.573 13.908 11388 Z= 0.295 Chirality : 0.044 0.452 1272 Planarity : 0.003 0.042 1452 Dihedral : 4.310 48.965 1142 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.80 % Allowed : 19.98 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1031 helix: 2.05 (0.26), residues: 399 sheet: 0.25 (0.35), residues: 183 loop : -0.50 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP R 310 HIS 0.003 0.001 HIS R 63 PHE 0.039 0.001 PHE A 70 TYR 0.015 0.001 TYR A 210 ARG 0.004 0.000 ARG N 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8432 (t0) cc_final: 0.8101 (m110) REVERT: A 157 LYS cc_start: 0.7752 (mmmt) cc_final: 0.7532 (mtpt) REVERT: B 101 MET cc_start: 0.8542 (mtp) cc_final: 0.8251 (mtp) REVERT: B 234 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8865 (m-80) REVERT: G 17 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7206 (pp20) REVERT: G 42 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: N 3 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: N 12 VAL cc_start: 0.8499 (p) cc_final: 0.8197 (m) REVERT: R 153 VAL cc_start: 0.8456 (t) cc_final: 0.8204 (m) outliers start: 16 outliers final: 9 residues processed: 131 average time/residue: 1.1641 time to fit residues: 162.6506 Evaluate side-chains 132 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 4 optimal weight: 0.1980 chunk 57 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.161401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.127590 restraints weight = 10425.893| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.45 r_work: 0.3401 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8408 Z= 0.168 Angle : 0.541 13.999 11388 Z= 0.281 Chirality : 0.042 0.420 1272 Planarity : 0.003 0.042 1452 Dihedral : 4.202 47.498 1142 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.68 % Allowed : 20.09 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1031 helix: 2.12 (0.26), residues: 399 sheet: 0.33 (0.35), residues: 173 loop : -0.55 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP R 310 HIS 0.003 0.001 HIS A 209 PHE 0.038 0.001 PHE A 70 TYR 0.013 0.001 TYR N 60 ARG 0.003 0.000 ARG N 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3316.20 seconds wall clock time: 58 minutes 48.15 seconds (3528.15 seconds total)