Starting phenix.real_space_refine on Sat Aug 3 13:33:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/08_2024/8w89_37349.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/08_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_37349/08_2024/8w89_37349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/08_2024/8w89_37349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/08_2024/8w89_37349.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/08_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-5409/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: 4.98, per 1000 atoms: 0.61 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: 3.14 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: 0.87 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: 2.34 Time building geometry restraints manager: 3.47 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 3.040 nonbonded pdb=" OG1 THR R 37 " pdb=" OG1 THR R 298 " model vdw 2.368 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.382 3.040 nonbonded pdb=" O SER R 115 " pdb=" OG SER R 118 " model vdw 2.407 3.040 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.430 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.010 Find NCS groups from input model: 0.080 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:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.260 ------------------------------------------------------------------------------- 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 : 1.171 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: 1.1792 time to fit residues: 204.4931 Evaluate side-chains 131 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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: 0.6980 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 220 GLN B 259 GLN R 53 GLN R 175 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8408 Z= 0.184 Angle : 0.541 6.815 11388 Z= 0.288 Chirality : 0.043 0.320 1272 Planarity : 0.004 0.047 1452 Dihedral : 4.507 57.268 1142 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.46 % Allowed : 12.12 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1031 helix: 2.31 (0.26), residues: 396 sheet: 0.20 (0.36), residues: 194 loop : -0.53 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS A 209 PHE 0.018 0.001 PHE A 70 TYR 0.017 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 163 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 THR cc_start: 0.8590 (p) cc_final: 0.8170 (p) REVERT: B 101 MET cc_start: 0.8403 (mtp) cc_final: 0.8146 (mtp) REVERT: B 153 ASP cc_start: 0.6397 (p0) cc_final: 0.6189 (m-30) REVERT: B 175 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7427 (mp10) REVERT: B 293 ASN cc_start: 0.7648 (m-40) cc_final: 0.7348 (p0) REVERT: N 12 VAL cc_start: 0.8519 (p) cc_final: 0.8257 (m) REVERT: R 143 MET cc_start: 0.8038 (mtt) cc_final: 0.7707 (mtm) REVERT: R 166 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7629 (mptp) REVERT: R 273 MET cc_start: 0.7695 (mmm) cc_final: 0.7434 (mmm) outliers start: 13 outliers final: 6 residues processed: 153 average time/residue: 1.0797 time to fit residues: 177.1815 Evaluate side-chains 139 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 B residue 243 THR 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: 8.9990 chunk 76 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 130 ASN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 259 GLN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8408 Z= 0.230 Angle : 0.535 5.765 11388 Z= 0.287 Chirality : 0.043 0.283 1272 Planarity : 0.004 0.039 1452 Dihedral : 4.579 59.072 1142 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.24 % Allowed : 14.59 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1031 helix: 2.24 (0.25), residues: 394 sheet: 0.08 (0.35), residues: 200 loop : -0.51 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS R 63 PHE 0.041 0.002 PHE A 70 TYR 0.021 0.001 TYR R 172 ARG 0.004 0.000 ARG N 19 *********************** 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 161 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7432 (mp10) REVERT: B 293 ASN cc_start: 0.7667 (m-40) cc_final: 0.7436 (p0) REVERT: G 42 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: N 12 VAL cc_start: 0.8545 (p) cc_final: 0.8247 (m) REVERT: R 77 MET cc_start: 0.8677 (mtm) cc_final: 0.8471 (mtt) REVERT: R 158 MET cc_start: 0.7116 (ttm) cc_final: 0.6543 (ttm) REVERT: R 166 LYS cc_start: 0.7568 (mmtt) cc_final: 0.7279 (mptp) outliers start: 20 outliers final: 9 residues processed: 147 average time/residue: 1.1073 time to fit residues: 173.9827 Evaluate side-chains 140 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 B residue 243 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 149 SER 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: 7.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1809 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= 0.161 Angle : 0.515 7.784 11388 Z= 0.271 Chirality : 0.042 0.356 1272 Planarity : 0.003 0.037 1452 Dihedral : 4.437 59.595 1142 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.13 % Allowed : 15.71 % Favored : 82.15 % 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: 1.19 (0.26), residues: 1031 helix: 2.44 (0.25), residues: 392 sheet: 0.20 (0.36), residues: 183 loop : -0.42 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.032 0.001 PHE A 70 TYR 0.023 0.001 TYR R 172 ARG 0.003 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 162 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 157 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7596 (mtpt) REVERT: B 101 MET cc_start: 0.8422 (mtp) cc_final: 0.8117 (mtp) REVERT: B 269 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8106 (mm) REVERT: G 17 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7160 (pp20) REVERT: N 12 VAL cc_start: 0.8486 (p) cc_final: 0.8209 (m) REVERT: R 77 MET cc_start: 0.8593 (mtm) cc_final: 0.8371 (mtt) REVERT: R 143 MET cc_start: 0.8058 (mtt) cc_final: 0.7750 (mtm) REVERT: R 166 LYS cc_start: 0.7366 (mmtt) cc_final: 0.7104 (mptp) outliers start: 19 outliers final: 6 residues processed: 149 average time/residue: 1.0971 time to fit residues: 174.7158 Evaluate side-chains 137 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 17 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 119 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8408 Z= 0.181 Angle : 0.520 6.977 11388 Z= 0.279 Chirality : 0.042 0.245 1272 Planarity : 0.003 0.035 1452 Dihedral : 4.401 59.137 1142 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.47 % Allowed : 16.84 % Favored : 80.70 % 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: 1.09 (0.26), residues: 1031 helix: 2.31 (0.26), residues: 393 sheet: 0.19 (0.36), residues: 173 loop : -0.44 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 87 PHE 0.043 0.001 PHE A 70 TYR 0.019 0.001 TYR R 172 ARG 0.004 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 152 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8428 (t0) cc_final: 0.8112 (m110) REVERT: B 101 MET cc_start: 0.8451 (mtp) cc_final: 0.8137 (mtp) REVERT: G 17 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7192 (pp20) REVERT: G 42 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: N 3 GLN cc_start: 0.7881 (pt0) cc_final: 0.7558 (tt0) REVERT: N 12 VAL cc_start: 0.8503 (p) cc_final: 0.8209 (m) REVERT: R 143 MET cc_start: 0.8062 (mtt) cc_final: 0.7736 (mtm) REVERT: R 166 LYS cc_start: 0.7246 (mmtt) cc_final: 0.7019 (mptp) outliers start: 22 outliers final: 11 residues processed: 141 average time/residue: 1.1855 time to fit residues: 177.7525 Evaluate side-chains 136 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR 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 81 MET Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 149 SER 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: 0.9990 chunk 19 optimal weight: 0.0030 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 144 ASN A 146 GLN B 259 GLN N 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2116 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= 0.202 Angle : 0.536 8.316 11388 Z= 0.285 Chirality : 0.043 0.354 1272 Planarity : 0.004 0.037 1452 Dihedral : 4.408 56.159 1142 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.47 % Allowed : 17.51 % Favored : 80.02 % 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: 2.20 (0.25), residues: 399 sheet: 0.12 (0.36), residues: 176 loop : -0.43 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 310 HIS 0.003 0.001 HIS R 63 PHE 0.044 0.002 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 147 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8434 (t0) cc_final: 0.8118 (m110) REVERT: B 101 MET cc_start: 0.8474 (mtp) cc_final: 0.8187 (mtp) REVERT: B 269 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8130 (mm) REVERT: G 42 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: N 3 GLN cc_start: 0.7880 (pt0) cc_final: 0.7504 (tt0) REVERT: N 12 VAL cc_start: 0.8513 (p) cc_final: 0.8214 (m) REVERT: R 52 LYS cc_start: 0.7610 (mtmp) cc_final: 0.7355 (mtmm) REVERT: R 158 MET cc_start: 0.7176 (ttm) cc_final: 0.6526 (ttm) outliers start: 22 outliers final: 10 residues processed: 134 average time/residue: 1.1412 time to fit residues: 163.0967 Evaluate side-chains 132 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE 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 81 MET Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.0570 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8408 Z= 0.170 Angle : 0.531 11.913 11388 Z= 0.281 Chirality : 0.043 0.411 1272 Planarity : 0.003 0.039 1452 Dihedral : 4.313 55.549 1142 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.91 % Allowed : 19.19 % 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: 1.09 (0.26), residues: 1031 helix: 2.28 (0.26), residues: 393 sheet: 0.18 (0.36), residues: 175 loop : -0.41 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 310 HIS 0.003 0.001 HIS R 87 PHE 0.039 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 144 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8411 (t0) cc_final: 0.8100 (m110) REVERT: A 157 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7575 (mtpt) REVERT: B 101 MET cc_start: 0.8428 (mtp) cc_final: 0.8145 (mtp) REVERT: B 234 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8840 (m-80) REVERT: B 269 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8127 (mm) REVERT: G 17 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7220 (pp20) REVERT: G 42 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: N 3 GLN cc_start: 0.7908 (pt0) cc_final: 0.7539 (tt0) REVERT: N 12 VAL cc_start: 0.8494 (p) cc_final: 0.8195 (m) REVERT: R 52 LYS cc_start: 0.7612 (mtmp) cc_final: 0.7363 (mtmm) REVERT: R 143 MET cc_start: 0.8066 (mtt) cc_final: 0.7793 (mtm) REVERT: R 158 MET cc_start: 0.7052 (ttm) cc_final: 0.6422 (ttm) REVERT: R 166 LYS cc_start: 0.6714 (mptp) cc_final: 0.6484 (mptp) outliers start: 17 outliers final: 11 residues processed: 137 average time/residue: 1.2629 time to fit residues: 185.1214 Evaluate side-chains 136 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE 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 81 MET Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 overall best weight: 0.4928 ------------------------------------------------------------------------------- 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 N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 8408 Z= 0.162 Angle : 0.531 13.384 11388 Z= 0.280 Chirality : 0.042 0.401 1272 Planarity : 0.003 0.040 1452 Dihedral : 4.227 54.192 1142 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.02 % Allowed : 18.86 % Favored : 79.12 % 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: 2.12 (0.26), residues: 400 sheet: 0.17 (0.36), residues: 176 loop : -0.39 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 310 HIS 0.003 0.001 HIS R 87 PHE 0.037 0.001 PHE A 70 TYR 0.011 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 149 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8400 (t0) cc_final: 0.8091 (m110) REVERT: A 157 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7603 (mtpt) REVERT: B 101 MET cc_start: 0.8393 (mtp) cc_final: 0.8135 (mtp) REVERT: B 234 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8853 (m-80) REVERT: G 17 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7228 (pp20) REVERT: G 42 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: N 3 GLN cc_start: 0.7917 (pt0) cc_final: 0.7544 (tt0) REVERT: N 12 VAL cc_start: 0.8473 (p) cc_final: 0.8182 (m) REVERT: R 143 MET cc_start: 0.8062 (mtt) cc_final: 0.7801 (mtm) REVERT: R 158 MET cc_start: 0.7006 (ttm) cc_final: 0.6398 (ttm) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 1.1717 time to fit residues: 176.0767 Evaluate side-chains 137 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR 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 81 MET Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 146 GLN B 75 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8408 Z= 0.180 Angle : 0.542 11.987 11388 Z= 0.287 Chirality : 0.043 0.396 1272 Planarity : 0.003 0.041 1452 Dihedral : 4.223 52.418 1142 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.68 % Allowed : 19.87 % Favored : 78.45 % 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: 2.23 (0.26), residues: 393 sheet: 0.18 (0.36), residues: 173 loop : -0.40 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 310 HIS 0.003 0.001 HIS R 87 PHE 0.036 0.001 PHE A 70 TYR 0.013 0.001 TYR A 191 ARG 0.005 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 136 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8406 (t0) cc_final: 0.8091 (m110) REVERT: A 157 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7605 (mtpt) REVERT: B 101 MET cc_start: 0.8437 (mtp) cc_final: 0.8220 (mtp) REVERT: B 234 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8876 (m-80) REVERT: G 17 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7240 (pp20) REVERT: G 42 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: N 3 GLN cc_start: 0.7914 (pt0) cc_final: 0.7537 (tt0) REVERT: N 12 VAL cc_start: 0.8461 (p) cc_final: 0.8169 (m) outliers start: 15 outliers final: 10 residues processed: 131 average time/residue: 1.2068 time to fit residues: 168.2202 Evaluate side-chains 130 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR 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 96 CYS Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 340 ASN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2323 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= 0.218 Angle : 0.568 13.249 11388 Z= 0.300 Chirality : 0.044 0.433 1272 Planarity : 0.004 0.042 1452 Dihedral : 4.331 49.838 1142 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.46 % Allowed : 19.98 % Favored : 78.56 % 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: 2.15 (0.25), residues: 393 sheet: 0.08 (0.36), residues: 174 loop : -0.41 (0.29), residues: 464 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 0.036 0.002 PHE A 70 TYR 0.016 0.001 TYR A 210 ARG 0.005 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: 13 poor density : 123 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8434 (t0) cc_final: 0.8115 (m110) REVERT: B 101 MET cc_start: 0.8488 (mtp) cc_final: 0.8147 (mtp) REVERT: G 17 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7264 (pp20) REVERT: G 42 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: N 3 GLN cc_start: 0.7896 (pt0) cc_final: 0.7483 (tt0) REVERT: N 12 VAL cc_start: 0.8486 (p) cc_final: 0.8180 (m) outliers start: 13 outliers final: 10 residues processed: 132 average time/residue: 1.1704 time to fit residues: 164.6373 Evaluate side-chains 129 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR 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 96 CYS Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 0.1980 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 4 optimal weight: 0.0030 chunk 57 optimal weight: 5.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.161104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126999 restraints weight = 10390.718| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.43 r_work: 0.3396 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2404 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= 0.179 Angle : 0.555 14.494 11388 Z= 0.292 Chirality : 0.043 0.437 1272 Planarity : 0.003 0.041 1452 Dihedral : 4.222 48.829 1142 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.35 % Allowed : 20.43 % 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: 2.20 (0.26), residues: 393 sheet: 0.16 (0.36), residues: 175 loop : -0.42 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP R 310 HIS 0.003 0.001 HIS R 87 PHE 0.035 0.001 PHE A 70 TYR 0.013 0.001 TYR A 191 ARG 0.005 0.000 ARG N 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.29 seconds wall clock time: 58 minutes 50.55 seconds (3530.55 seconds total)