Starting phenix.real_space_refine on Mon Dec 30 22:25:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zxe_15009/12_2024/7zxe_15009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zxe_15009/12_2024/7zxe_15009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zxe_15009/12_2024/7zxe_15009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zxe_15009/12_2024/7zxe_15009.map" model { file = "/net/cci-nas-00/data/ceres_data/7zxe_15009/12_2024/7zxe_15009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zxe_15009/12_2024/7zxe_15009.cif" } resolution = 3.5 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= 0.002 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 93 5.49 5 S 68 5.16 5 C 8676 2.51 5 N 2504 2.21 5 O 2807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14150 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1567 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 10, 'TRANS': 190} Chain: "N" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 987 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "T" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 921 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "U" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "a" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1807 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "b" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2977 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2516 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 1 Chain: "d" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 424 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9621 SG CYS b 221 76.488 68.528 26.048 1.00139.75 S ATOM 10418 SG CYS b 317 72.705 68.101 26.856 1.00147.72 S ATOM 10740 SG CYS b 354 88.563 47.824 28.607 1.00133.30 S ATOM 10764 SG CYS b 357 92.447 47.927 28.524 1.00131.82 S ATOM 10955 SG CYS b 380 90.426 48.557 25.390 1.00131.89 S ATOM 10976 SG CYS b 383 90.645 45.098 26.867 1.00134.69 S Time building chain proxies: 9.08, per 1000 atoms: 0.64 Number of scatterers: 14150 At special positions: 0 Unit cell: (135.45, 164.85, 110.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 68 16.00 P 93 15.00 O 2807 8.00 N 2504 7.00 C 8676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.86 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 501 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 313 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 319 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 317 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 221 " pdb=" ZN b 502 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 380 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 383 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 357 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 354 " Number of angles added : 8 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2874 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 53.3% alpha, 11.4% beta 38 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 5.05 Creating SS restraints... Processing helix chain 'M' and resid 117 through 129 removed outlier: 3.866A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.800A pdb=" N VAL M 135 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 187 through 203 Processing helix chain 'M' and resid 211 through 222 removed outlier: 4.067A pdb=" N MET M 215 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG M 217 " --> pdb=" O ASP M 213 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER M 220 " --> pdb=" O SER M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 265 Processing helix chain 'M' and resid 270 through 279 removed outlier: 3.828A pdb=" N ILE M 274 " --> pdb=" O THR M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 292 removed outlier: 3.640A pdb=" N ILE M 292 " --> pdb=" O SER M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.773A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 295 through 300' Processing helix chain 'O' and resid 179 through 187 Processing helix chain 'O' and resid 226 through 244 Processing helix chain 'O' and resid 269 through 277 Processing helix chain 'O' and resid 317 through 335 removed outlier: 3.506A pdb=" N ILE O 321 " --> pdb=" O VAL O 317 " (cutoff:3.500A) Proline residue: O 330 - end of helix Processing helix chain 'U' and resid 10 through 33 removed outlier: 4.422A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 51 removed outlier: 3.654A pdb=" N LEU U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 29 through 49 Processing helix chain 'a' and resid 6 through 20 removed outlier: 4.582A pdb=" N ASP a 10 " --> pdb=" O GLY a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 37 removed outlier: 3.903A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 42 removed outlier: 3.993A pdb=" N PHE a 42 " --> pdb=" O GLY a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 67 Processing helix chain 'a' and resid 71 through 88 Processing helix chain 'a' and resid 100 through 117 removed outlier: 4.186A pdb=" N ASP a 105 " --> pdb=" O LEU a 101 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 119 through 132 Processing helix chain 'a' and resid 166 through 172 removed outlier: 4.218A pdb=" N LYS a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 195 removed outlier: 3.686A pdb=" N SER a 195 " --> pdb=" O LYS a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 232 removed outlier: 4.384A pdb=" N ASP a 214 " --> pdb=" O ASP a 210 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 55 Processing helix chain 'b' and resid 77 through 91 removed outlier: 3.634A pdb=" N ARG b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 104 Processing helix chain 'b' and resid 127 through 144 Processing helix chain 'b' and resid 150 through 161 Processing helix chain 'b' and resid 192 through 196 removed outlier: 3.698A pdb=" N LYS b 196 " --> pdb=" O HIS b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 226 removed outlier: 3.717A pdb=" N GLN b 226 " --> pdb=" O SER b 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 242 through 247 Processing helix chain 'b' and resid 270 through 280 removed outlier: 4.448A pdb=" N ILE b 274 " --> pdb=" O LEU b 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 389 removed outlier: 3.650A pdb=" N TYR b 389 " --> pdb=" O ARG b 385 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 123 removed outlier: 4.229A pdb=" N CYS c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 162 through 171 Processing helix chain 'c' and resid 185 through 221 Proline residue: c 207 - end of helix Processing helix chain 'c' and resid 225 through 247 Processing helix chain 'c' and resid 249 through 255 removed outlier: 4.287A pdb=" N GLY c 255 " --> pdb=" O GLU c 251 " (cutoff:3.500A) Processing helix chain 'c' and resid 262 through 267 removed outlier: 3.808A pdb=" N ILE c 266 " --> pdb=" O ASP c 262 " (cutoff:3.500A) Processing helix chain 'c' and resid 276 through 287 Processing helix chain 'c' and resid 298 through 313 Processing helix chain 'c' and resid 316 through 324 Processing helix chain 'c' and resid 329 through 340 Processing helix chain 'c' and resid 350 through 365 Processing helix chain 'c' and resid 371 through 376 Processing helix chain 'c' and resid 383 through 394 Processing helix chain 'd' and resid 2 through 45 Processing sheet with id=AA1, first strand: chain 'O' and resid 190 through 191 removed outlier: 4.052A pdb=" N LYS O 218 " --> pdb=" O PHE O 214 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU O 165 " --> pdb=" O GLY O 260 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY O 260 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN O 167 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET O 258 " --> pdb=" O ASN O 167 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL O 169 " --> pdb=" O GLN O 256 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN O 173 " --> pdb=" O ASP O 252 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP O 252 " --> pdb=" O ASN O 173 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N MET O 258 " --> pdb=" O GLY O 314 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY O 314 " --> pdb=" O MET O 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 363 through 367 removed outlier: 4.280A pdb=" N PHE V 58 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE V 58 " --> pdb=" O PHE V 81 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE V 81 " --> pdb=" O PHE V 58 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY V 60 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL V 79 " --> pdb=" O GLY V 60 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU V 62 " --> pdb=" O ASN V 77 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN V 77 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASP V 91 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU V 80 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS V 89 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG V 82 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU V 87 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL U 335 " --> pdb=" O VAL V 96 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS V 98 " --> pdb=" O VAL U 335 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS U 337 " --> pdb=" O CYS V 98 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL U 335 " --> pdb=" O MET U 358 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET U 358 " --> pdb=" O VAL U 335 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS U 337 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY U 356 " --> pdb=" O CYS U 337 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR U 339 " --> pdb=" O LYS U 354 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS U 354 " --> pdb=" O TYR U 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'b' and resid 42 through 43 Processing sheet with id=AA5, first strand: chain 'b' and resid 290 through 291 removed outlier: 6.846A pdb=" N PHE b 258 " --> pdb=" O ALA b 291 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL b 320 " --> pdb=" O LEU b 187 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR b 324 " --> pdb=" O SER b 183 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER b 183 " --> pdb=" O THR b 324 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE b 326 " --> pdb=" O ILE b 181 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE b 181 " --> pdb=" O ILE b 326 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR b 203 " --> pdb=" O ILE b 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 377 through 379 652 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3567 1.33 - 1.45: 3101 1.45 - 1.57: 7662 1.57 - 1.69: 184 1.69 - 1.81: 105 Bond restraints: 14619 Sorted by residual: bond pdb=" N MET d 1 " pdb=" CA MET d 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" CG PRO b 308 " pdb=" CD PRO b 308 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.69e+00 bond pdb=" C3' DC T -6 " pdb=" O3' DC T -6 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" C1' DC T 24 " pdb=" N1 DC T 24 " ideal model delta sigma weight residual 1.490 1.521 -0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" C4' DC T -6 " pdb=" C3' DC T -6 " ideal model delta sigma weight residual 1.523 1.543 -0.020 2.00e-02 2.50e+03 1.03e+00 ... (remaining 14614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 19372 1.26 - 2.53: 596 2.53 - 3.79: 125 3.79 - 5.06: 16 5.06 - 6.32: 3 Bond angle restraints: 20112 Sorted by residual: angle pdb=" N ILE M 180 " pdb=" CA ILE M 180 " pdb=" C ILE M 180 " ideal model delta sigma weight residual 111.58 107.59 3.99 1.06e+00 8.90e-01 1.42e+01 angle pdb=" CA PRO b 308 " pdb=" N PRO b 308 " pdb=" CD PRO b 308 " ideal model delta sigma weight residual 112.00 107.85 4.15 1.40e+00 5.10e-01 8.80e+00 angle pdb=" N GLU a 31 " pdb=" CA GLU a 31 " pdb=" CB GLU a 31 " ideal model delta sigma weight residual 110.12 114.27 -4.15 1.47e+00 4.63e-01 7.98e+00 angle pdb=" C ARG V 82 " pdb=" N GLU V 83 " pdb=" CA GLU V 83 " ideal model delta sigma weight residual 122.03 116.91 5.12 2.01e+00 2.48e-01 6.49e+00 angle pdb=" C TYR c 141 " pdb=" N MET c 142 " pdb=" CA MET c 142 " ideal model delta sigma weight residual 120.29 123.88 -3.59 1.42e+00 4.96e-01 6.40e+00 ... (remaining 20107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 8000 31.18 - 62.36: 596 62.36 - 93.54: 35 93.54 - 124.72: 1 124.72 - 155.90: 2 Dihedral angle restraints: 8634 sinusoidal: 4224 harmonic: 4410 Sorted by residual: dihedral pdb=" CA VAL V 52 " pdb=" C VAL V 52 " pdb=" N ARG V 53 " pdb=" CA ARG V 53 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TYR b 32 " pdb=" C TYR b 32 " pdb=" N GLU b 33 " pdb=" CA GLU b 33 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 8631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1739 0.041 - 0.081: 353 0.081 - 0.122: 99 0.122 - 0.162: 14 0.162 - 0.203: 1 Chirality restraints: 2206 Sorted by residual: chirality pdb=" CG LEU d 22 " pdb=" CB LEU d 22 " pdb=" CD1 LEU d 22 " pdb=" CD2 LEU d 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE b 321 " pdb=" N ILE b 321 " pdb=" C ILE b 321 " pdb=" CB ILE b 321 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA ILE b 186 " pdb=" N ILE b 186 " pdb=" C ILE b 186 " pdb=" CB ILE b 186 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 2203 not shown) Planarity restraints: 2263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE b 307 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO b 308 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO b 308 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO b 308 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 130 " 0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO M 131 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO M 131 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO M 131 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 226 " 0.010 2.00e-02 2.50e+03 1.01e-02 2.55e+00 pdb=" CG TRP a 226 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP a 226 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP a 226 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 226 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP a 226 " -0.002 2.00e-02 2.50e+03 ... (remaining 2260 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 142 2.56 - 3.15: 11688 3.15 - 3.73: 23746 3.73 - 4.32: 32168 4.32 - 4.90: 51251 Nonbonded interactions: 118995 Sorted by model distance: nonbonded pdb=" O LEU a 207 " pdb=" NH2 ARG d 28 " model vdw 1.978 3.120 nonbonded pdb=" OP1 DG N 8 " pdb=" OG SER O 216 " model vdw 2.016 3.040 nonbonded pdb=" OH TYR V 3 " pdb=" O CYS V 98 " model vdw 2.044 3.040 nonbonded pdb=" O SER M 216 " pdb=" OG SER M 220 " model vdw 2.095 3.040 nonbonded pdb=" OG SER b 209 " pdb=" OD1 ASN b 299 " model vdw 2.104 3.040 ... (remaining 118990 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 3.650 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.850 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.003 0.047 14619 Z= 0.164 Angle : 0.548 6.319 20112 Z= 0.323 Chirality : 0.037 0.203 2206 Planarity : 0.004 0.103 2263 Dihedral : 19.337 155.905 5760 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.71 (0.23), residues: 1474 helix: 1.79 (0.20), residues: 747 sheet: -0.34 (0.42), residues: 136 loop : -1.07 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP a 226 HIS 0.006 0.001 HIS c 369 PHE 0.025 0.001 PHE V 81 TYR 0.018 0.001 TYR c 141 ARG 0.006 0.000 ARG V 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 129 ASN cc_start: 0.8640 (m110) cc_final: 0.7964 (t0) REVERT: M 227 GLN cc_start: 0.9361 (mp10) cc_final: 0.9150 (mp10) REVERT: M 259 TYR cc_start: 0.9308 (t80) cc_final: 0.8919 (t80) REVERT: O 229 GLN cc_start: 0.8435 (mp10) cc_final: 0.8199 (mp10) REVERT: U 24 ASP cc_start: 0.8080 (p0) cc_final: 0.7791 (p0) REVERT: U 35 ASP cc_start: 0.7804 (p0) cc_final: 0.7463 (p0) REVERT: U 37 GLN cc_start: 0.9118 (mp-120) cc_final: 0.8340 (mp10) REVERT: U 43 LYS cc_start: 0.9262 (ttpp) cc_final: 0.9013 (ttpt) REVERT: U 47 GLU cc_start: 0.8976 (mp0) cc_final: 0.8634 (mp0) REVERT: V 21 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8670 (mm-30) REVERT: V 83 GLU cc_start: 0.7587 (pp20) cc_final: 0.7384 (pp20) REVERT: a 53 MET cc_start: 0.8920 (tmm) cc_final: 0.8687 (tmm) REVERT: a 57 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8201 (tt0) REVERT: a 83 TYR cc_start: 0.8783 (t80) cc_final: 0.8368 (t80) REVERT: a 119 HIS cc_start: 0.8874 (m-70) cc_final: 0.8161 (m90) REVERT: a 226 TRP cc_start: 0.8955 (t60) cc_final: 0.8739 (t60) REVERT: c 248 LEU cc_start: 0.9070 (tp) cc_final: 0.8769 (tp) REVERT: c 259 ASP cc_start: 0.7831 (p0) cc_final: 0.7522 (p0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2584 time to fit residues: 80.7003 Evaluate side-chains 140 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 256 GLN a 188 GLN b 139 HIS ** c 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 14619 Z= 0.484 Angle : 0.800 10.262 20112 Z= 0.430 Chirality : 0.048 0.212 2206 Planarity : 0.006 0.073 2263 Dihedral : 22.418 150.923 2641 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.87 % Allowed : 8.24 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.04 (0.21), residues: 1474 helix: 1.09 (0.18), residues: 760 sheet: -0.58 (0.44), residues: 111 loop : -1.23 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 226 HIS 0.014 0.002 HIS U 343 PHE 0.025 0.002 PHE U 351 TYR 0.026 0.002 TYR O 237 ARG 0.015 0.001 ARG d 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 227 GLN cc_start: 0.9400 (mp10) cc_final: 0.9113 (pm20) REVERT: M 304 PHE cc_start: 0.8708 (t80) cc_final: 0.8438 (t80) REVERT: O 191 GLU cc_start: 0.8039 (tp30) cc_final: 0.7805 (tp30) REVERT: O 229 GLN cc_start: 0.8512 (mp10) cc_final: 0.8161 (mp10) REVERT: O 286 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8059 (tm-30) REVERT: U 24 ASP cc_start: 0.8280 (p0) cc_final: 0.8061 (p0) REVERT: U 37 GLN cc_start: 0.9227 (mp-120) cc_final: 0.8612 (mp10) REVERT: U 40 MET cc_start: 0.8866 (ptt) cc_final: 0.8498 (ptt) REVERT: U 346 LYS cc_start: 0.8564 (tptt) cc_final: 0.8351 (tptt) REVERT: V 35 GLN cc_start: 0.8823 (mp10) cc_final: 0.8548 (mp10) REVERT: V 56 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8173 (t) REVERT: V 83 GLU cc_start: 0.7900 (pp20) cc_final: 0.7473 (pp20) REVERT: V 84 VAL cc_start: 0.8958 (t) cc_final: 0.8262 (p) REVERT: a 27 GLU cc_start: 0.8993 (mp0) cc_final: 0.8787 (pm20) REVERT: a 35 ASN cc_start: 0.9399 (m110) cc_final: 0.9110 (m110) REVERT: a 57 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8488 (tt0) REVERT: a 119 HIS cc_start: 0.9046 (m-70) cc_final: 0.8098 (m90) REVERT: b 143 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8523 (p) REVERT: b 204 MET cc_start: 0.8924 (mtp) cc_final: 0.8480 (mmm) REVERT: b 340 TYR cc_start: 0.7327 (t80) cc_final: 0.6791 (t80) REVERT: c 248 LEU cc_start: 0.9122 (tp) cc_final: 0.8853 (tp) outliers start: 25 outliers final: 18 residues processed: 170 average time/residue: 0.2707 time to fit residues: 69.0333 Evaluate side-chains 150 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain U residue 18 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 289 GLN Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain c residue 216 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 140 optimal weight: 0.0270 chunk 151 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 116 ASN M 221 ASN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 GLN ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 232 ASN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 144 HIS c 268 ASN c 369 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14619 Z= 0.190 Angle : 0.605 10.122 20112 Z= 0.328 Chirality : 0.040 0.157 2206 Planarity : 0.004 0.064 2263 Dihedral : 22.089 146.855 2641 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.20 % Allowed : 11.61 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.44 (0.22), residues: 1474 helix: 1.50 (0.19), residues: 758 sheet: -0.59 (0.43), residues: 118 loop : -1.10 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 226 HIS 0.006 0.001 HIS a 227 PHE 0.015 0.001 PHE U 351 TYR 0.014 0.001 TYR b 340 ARG 0.004 0.000 ARG M 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 227 GLN cc_start: 0.9391 (mp10) cc_final: 0.9141 (mp10) REVERT: M 229 GLN cc_start: 0.9207 (tp40) cc_final: 0.8613 (tp40) REVERT: M 244 LEU cc_start: 0.9211 (mt) cc_final: 0.8759 (tp) REVERT: M 259 TYR cc_start: 0.9390 (t80) cc_final: 0.8987 (t80) REVERT: M 271 GLN cc_start: 0.9307 (mt0) cc_final: 0.8942 (mt0) REVERT: O 237 TYR cc_start: 0.7973 (m-80) cc_final: 0.7679 (m-80) REVERT: O 286 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7760 (tm-30) REVERT: U 24 ASP cc_start: 0.8250 (p0) cc_final: 0.7948 (p0) REVERT: U 35 ASP cc_start: 0.7890 (p0) cc_final: 0.6798 (p0) REVERT: U 37 GLN cc_start: 0.9278 (mp-120) cc_final: 0.8483 (mp10) REVERT: U 40 MET cc_start: 0.8776 (ptt) cc_final: 0.8496 (ptt) REVERT: U 341 LYS cc_start: 0.8355 (tptm) cc_final: 0.8077 (tptt) REVERT: U 373 ASP cc_start: 0.8391 (t0) cc_final: 0.8178 (t0) REVERT: V 83 GLU cc_start: 0.7867 (pp20) cc_final: 0.7388 (pp20) REVERT: V 84 VAL cc_start: 0.8869 (t) cc_final: 0.8111 (p) REVERT: a 35 ASN cc_start: 0.9386 (m110) cc_final: 0.9094 (m110) REVERT: a 57 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8325 (tt0) REVERT: a 119 HIS cc_start: 0.8881 (m-70) cc_final: 0.8536 (m90) REVERT: b 204 MET cc_start: 0.8712 (mtp) cc_final: 0.8400 (mmm) REVERT: b 340 TYR cc_start: 0.7279 (t80) cc_final: 0.6928 (t80) REVERT: c 248 LEU cc_start: 0.9118 (tp) cc_final: 0.8826 (tp) outliers start: 16 outliers final: 9 residues processed: 177 average time/residue: 0.2512 time to fit residues: 67.6213 Evaluate side-chains 152 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain c residue 164 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 GLN ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 237 GLN ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14619 Z= 0.325 Angle : 0.664 9.649 20112 Z= 0.354 Chirality : 0.042 0.168 2206 Planarity : 0.005 0.062 2263 Dihedral : 22.211 151.704 2641 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.02 % Allowed : 13.71 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.31 (0.22), residues: 1474 helix: 1.34 (0.19), residues: 765 sheet: -0.49 (0.45), residues: 118 loop : -1.16 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP a 226 HIS 0.020 0.001 HIS a 227 PHE 0.014 0.002 PHE a 54 TYR 0.019 0.002 TYR b 340 ARG 0.007 0.001 ARG V 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 124 MET cc_start: 0.8824 (mmt) cc_final: 0.8509 (mmt) REVERT: M 144 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8392 (mp10) REVERT: M 227 GLN cc_start: 0.9422 (mp10) cc_final: 0.8987 (pm20) REVERT: M 229 GLN cc_start: 0.9275 (tp40) cc_final: 0.8724 (tp40) REVERT: M 259 TYR cc_start: 0.9440 (t80) cc_final: 0.8996 (t80) REVERT: M 271 GLN cc_start: 0.9312 (mt0) cc_final: 0.9058 (mt0) REVERT: O 237 TYR cc_start: 0.8107 (m-80) cc_final: 0.7799 (m-80) REVERT: O 286 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7920 (tm-30) REVERT: U 20 ASP cc_start: 0.9052 (t0) cc_final: 0.8850 (t0) REVERT: U 24 ASP cc_start: 0.8115 (p0) cc_final: 0.7691 (p0) REVERT: U 37 GLN cc_start: 0.9312 (mp-120) cc_final: 0.8794 (mm-40) REVERT: U 40 MET cc_start: 0.8735 (ptt) cc_final: 0.8179 (ptt) REVERT: U 341 LYS cc_start: 0.8394 (tptm) cc_final: 0.8162 (tptt) REVERT: V 89 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8870 (tptt) REVERT: a 35 ASN cc_start: 0.9411 (m110) cc_final: 0.9099 (m-40) REVERT: a 57 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8380 (tt0) REVERT: a 119 HIS cc_start: 0.8994 (m-70) cc_final: 0.8619 (m90) REVERT: b 204 MET cc_start: 0.8848 (mtp) cc_final: 0.8397 (mmm) REVERT: b 340 TYR cc_start: 0.7563 (t80) cc_final: 0.7030 (t80) REVERT: c 248 LEU cc_start: 0.9156 (tp) cc_final: 0.8880 (tp) REVERT: c 356 MET cc_start: 0.9017 (tpp) cc_final: 0.8294 (tpp) outliers start: 27 outliers final: 20 residues processed: 168 average time/residue: 0.2595 time to fit residues: 66.3654 Evaluate side-chains 152 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 338 GLN Chi-restraints excluded: chain U residue 351 PHE Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 216 HIS Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 48 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 299 ASN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14619 Z= 0.242 Angle : 0.627 10.855 20112 Z= 0.332 Chirality : 0.041 0.236 2206 Planarity : 0.004 0.064 2263 Dihedral : 22.117 152.938 2641 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.10 % Allowed : 14.46 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.43 (0.22), residues: 1474 helix: 1.44 (0.19), residues: 764 sheet: -0.44 (0.45), residues: 118 loop : -1.09 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP a 226 HIS 0.021 0.001 HIS a 227 PHE 0.013 0.001 PHE U 351 TYR 0.019 0.001 TYR a 83 ARG 0.007 0.000 ARG d 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 124 MET cc_start: 0.8778 (mmt) cc_final: 0.8549 (mmt) REVERT: M 227 GLN cc_start: 0.9400 (mp10) cc_final: 0.8971 (pm20) REVERT: M 259 TYR cc_start: 0.9439 (t80) cc_final: 0.8974 (t80) REVERT: M 271 GLN cc_start: 0.9315 (mt0) cc_final: 0.9004 (mt0) REVERT: O 237 TYR cc_start: 0.8079 (m-80) cc_final: 0.7800 (m-80) REVERT: O 286 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7843 (tm-30) REVERT: U 24 ASP cc_start: 0.8176 (p0) cc_final: 0.7928 (p0) REVERT: U 35 ASP cc_start: 0.8069 (p0) cc_final: 0.6754 (p0) REVERT: U 36 GLU cc_start: 0.8622 (tp30) cc_final: 0.7041 (tp30) REVERT: U 37 GLN cc_start: 0.9273 (mp-120) cc_final: 0.8267 (mp10) REVERT: U 341 LYS cc_start: 0.8352 (tptm) cc_final: 0.8138 (tptt) REVERT: V 89 LYS cc_start: 0.9172 (mmmm) cc_final: 0.8883 (tptt) REVERT: a 35 ASN cc_start: 0.9398 (m110) cc_final: 0.9094 (m110) REVERT: a 57 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8406 (tt0) REVERT: a 119 HIS cc_start: 0.8949 (m-70) cc_final: 0.8641 (m90) REVERT: b 204 MET cc_start: 0.8807 (mtp) cc_final: 0.8512 (mmm) REVERT: b 340 TYR cc_start: 0.7425 (t80) cc_final: 0.7053 (t80) REVERT: b 386 MET cc_start: 0.9218 (mmm) cc_final: 0.8831 (mmm) REVERT: c 248 LEU cc_start: 0.9156 (tp) cc_final: 0.8878 (tp) REVERT: c 315 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6356 (tp) REVERT: c 356 MET cc_start: 0.9000 (tpp) cc_final: 0.8295 (tpp) outliers start: 28 outliers final: 16 residues processed: 168 average time/residue: 0.2534 time to fit residues: 64.7026 Evaluate side-chains 160 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 338 GLN Chi-restraints excluded: chain U residue 351 PHE Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 80 GLU Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.0370 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 237 GLN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14619 Z= 0.188 Angle : 0.636 12.508 20112 Z= 0.333 Chirality : 0.040 0.296 2206 Planarity : 0.004 0.062 2263 Dihedral : 22.043 153.989 2641 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.80 % Allowed : 15.73 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.50 (0.22), residues: 1474 helix: 1.45 (0.19), residues: 769 sheet: -0.30 (0.46), residues: 118 loop : -1.04 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 226 HIS 0.004 0.001 HIS a 227 PHE 0.019 0.001 PHE U 351 TYR 0.011 0.001 TYR b 340 ARG 0.007 0.000 ARG d 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 221 ASN cc_start: 0.9323 (m-40) cc_final: 0.8842 (m110) REVERT: M 227 GLN cc_start: 0.9349 (mp10) cc_final: 0.9015 (mp10) REVERT: M 229 GLN cc_start: 0.9313 (tp40) cc_final: 0.9047 (tp40) REVERT: M 244 LEU cc_start: 0.9207 (mt) cc_final: 0.8680 (tp) REVERT: M 259 TYR cc_start: 0.9422 (t80) cc_final: 0.8927 (t80) REVERT: M 271 GLN cc_start: 0.9308 (mt0) cc_final: 0.8959 (mt0) REVERT: O 237 TYR cc_start: 0.8031 (m-80) cc_final: 0.7784 (m-80) REVERT: O 286 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7702 (tm-30) REVERT: U 35 ASP cc_start: 0.8009 (p0) cc_final: 0.6714 (p0) REVERT: U 37 GLN cc_start: 0.9019 (mp-120) cc_final: 0.8347 (mp10) REVERT: U 341 LYS cc_start: 0.8288 (tptm) cc_final: 0.8087 (tptt) REVERT: V 89 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8820 (tptt) REVERT: a 35 ASN cc_start: 0.9376 (m110) cc_final: 0.9085 (m-40) REVERT: a 57 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8365 (tt0) REVERT: a 119 HIS cc_start: 0.8930 (m-70) cc_final: 0.8633 (m90) REVERT: b 204 MET cc_start: 0.8815 (mtp) cc_final: 0.8541 (mmm) REVERT: c 248 LEU cc_start: 0.9169 (tp) cc_final: 0.8889 (tp) REVERT: c 315 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6268 (tp) REVERT: c 356 MET cc_start: 0.8996 (tpp) cc_final: 0.8356 (tpp) outliers start: 24 outliers final: 19 residues processed: 171 average time/residue: 0.2801 time to fit residues: 71.5947 Evaluate side-chains 164 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 80 GLU Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 175 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 216 HIS Chi-restraints excluded: chain c residue 315 LEU Chi-restraints excluded: chain d residue 22 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 90 optimal weight: 0.0770 chunk 68 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14619 Z= 0.186 Angle : 0.634 11.608 20112 Z= 0.332 Chirality : 0.040 0.188 2206 Planarity : 0.004 0.061 2263 Dihedral : 21.993 155.169 2641 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.02 % Allowed : 16.78 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.62 (0.22), residues: 1474 helix: 1.53 (0.19), residues: 767 sheet: -0.07 (0.47), residues: 111 loop : -0.98 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP a 226 HIS 0.026 0.001 HIS a 227 PHE 0.018 0.001 PHE U 351 TYR 0.010 0.001 TYR V 65 ARG 0.006 0.000 ARG O 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 221 ASN cc_start: 0.9310 (m-40) cc_final: 0.8835 (m110) REVERT: M 227 GLN cc_start: 0.9358 (mp10) cc_final: 0.8988 (mp10) REVERT: M 229 GLN cc_start: 0.9318 (tp40) cc_final: 0.9033 (tp40) REVERT: M 259 TYR cc_start: 0.9423 (t80) cc_final: 0.8936 (t80) REVERT: M 271 GLN cc_start: 0.9322 (mt0) cc_final: 0.8922 (mt0) REVERT: O 286 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7678 (tm-30) REVERT: U 35 ASP cc_start: 0.8151 (p0) cc_final: 0.7183 (p0) REVERT: U 37 GLN cc_start: 0.9101 (mp-120) cc_final: 0.8506 (mp10) REVERT: U 40 MET cc_start: 0.8667 (mmm) cc_final: 0.8400 (mmm) REVERT: V 89 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8782 (tptt) REVERT: a 11 CYS cc_start: 0.9463 (m) cc_final: 0.9024 (m) REVERT: a 35 ASN cc_start: 0.9374 (m110) cc_final: 0.9092 (m-40) REVERT: a 57 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8371 (tt0) REVERT: b 204 MET cc_start: 0.8822 (mtp) cc_final: 0.8359 (mmm) REVERT: b 340 TYR cc_start: 0.7092 (t80) cc_final: 0.6867 (t80) REVERT: c 248 LEU cc_start: 0.9170 (tp) cc_final: 0.8891 (tp) REVERT: c 315 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6215 (tp) REVERT: c 356 MET cc_start: 0.9010 (tpp) cc_final: 0.8361 (tpp) REVERT: d 9 ARG cc_start: 0.8050 (tmm160) cc_final: 0.7761 (ptm-80) outliers start: 27 outliers final: 18 residues processed: 175 average time/residue: 0.2513 time to fit residues: 66.7348 Evaluate side-chains 163 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 351 PHE Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 80 GLU Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 175 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 216 HIS Chi-restraints excluded: chain c residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 GLN ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14619 Z= 0.196 Angle : 0.652 15.174 20112 Z= 0.339 Chirality : 0.040 0.187 2206 Planarity : 0.004 0.070 2263 Dihedral : 21.984 155.968 2641 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.50 % Allowed : 17.53 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.63 (0.22), residues: 1474 helix: 1.47 (0.19), residues: 768 sheet: 0.23 (0.48), residues: 106 loop : -0.94 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP a 226 HIS 0.004 0.001 HIS a 119 PHE 0.018 0.001 PHE O 325 TYR 0.023 0.001 TYR a 83 ARG 0.015 0.000 ARG V 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 221 ASN cc_start: 0.9287 (m-40) cc_final: 0.8833 (m110) REVERT: M 227 GLN cc_start: 0.9383 (mp10) cc_final: 0.9103 (pm20) REVERT: M 229 GLN cc_start: 0.9324 (tp40) cc_final: 0.9032 (tp40) REVERT: M 259 TYR cc_start: 0.9420 (t80) cc_final: 0.8936 (t80) REVERT: M 271 GLN cc_start: 0.9342 (mt0) cc_final: 0.8924 (mt0) REVERT: O 286 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7668 (tm-30) REVERT: U 35 ASP cc_start: 0.8097 (p0) cc_final: 0.6998 (p0) REVERT: U 37 GLN cc_start: 0.9148 (mp-120) cc_final: 0.8580 (mp10) REVERT: U 355 ASP cc_start: 0.8308 (p0) cc_final: 0.8084 (p0) REVERT: V 35 GLN cc_start: 0.8870 (mp10) cc_final: 0.8551 (mp10) REVERT: V 89 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8805 (tptt) REVERT: a 11 CYS cc_start: 0.9454 (m) cc_final: 0.9024 (m) REVERT: a 35 ASN cc_start: 0.9379 (m110) cc_final: 0.9111 (m110) REVERT: a 57 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8392 (tt0) REVERT: b 174 MET cc_start: 0.7829 (tpp) cc_final: 0.7474 (tpp) REVERT: b 204 MET cc_start: 0.8847 (mtp) cc_final: 0.8326 (mmm) REVERT: b 340 TYR cc_start: 0.7346 (t80) cc_final: 0.7134 (t80) REVERT: c 248 LEU cc_start: 0.9163 (tp) cc_final: 0.8887 (tp) REVERT: c 315 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6214 (tp) REVERT: c 356 MET cc_start: 0.9017 (tpp) cc_final: 0.8401 (tpp) REVERT: d 9 ARG cc_start: 0.8104 (tmm160) cc_final: 0.7469 (ptm-80) outliers start: 20 outliers final: 18 residues processed: 160 average time/residue: 0.2543 time to fit residues: 62.4468 Evaluate side-chains 156 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 175 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 216 HIS Chi-restraints excluded: chain c residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 83 optimal weight: 0.0370 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14619 Z= 0.192 Angle : 0.662 15.019 20112 Z= 0.345 Chirality : 0.040 0.194 2206 Planarity : 0.004 0.059 2263 Dihedral : 21.955 156.744 2641 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.57 % Allowed : 17.75 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.67 (0.22), residues: 1474 helix: 1.51 (0.19), residues: 768 sheet: 0.10 (0.47), residues: 111 loop : -0.90 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP a 226 HIS 0.003 0.001 HIS a 223 PHE 0.016 0.001 PHE U 351 TYR 0.022 0.001 TYR a 83 ARG 0.012 0.000 ARG V 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 221 ASN cc_start: 0.9262 (m-40) cc_final: 0.8804 (m110) REVERT: M 227 GLN cc_start: 0.9386 (mp10) cc_final: 0.8994 (mp10) REVERT: M 229 GLN cc_start: 0.9325 (tp40) cc_final: 0.9033 (tp40) REVERT: M 259 TYR cc_start: 0.9413 (t80) cc_final: 0.8924 (t80) REVERT: M 271 GLN cc_start: 0.9348 (mt0) cc_final: 0.8928 (mt0) REVERT: O 286 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7640 (tm-30) REVERT: O 295 MET cc_start: 0.8449 (ttm) cc_final: 0.8217 (ttm) REVERT: U 35 ASP cc_start: 0.8006 (p0) cc_final: 0.6947 (p0) REVERT: U 37 GLN cc_start: 0.9105 (mp-120) cc_final: 0.8551 (mp10) REVERT: U 355 ASP cc_start: 0.8322 (p0) cc_final: 0.8106 (p0) REVERT: V 35 GLN cc_start: 0.8880 (mp10) cc_final: 0.8529 (mp10) REVERT: V 89 LYS cc_start: 0.9109 (mmmm) cc_final: 0.8786 (tptt) REVERT: a 11 CYS cc_start: 0.9463 (m) cc_final: 0.9035 (m) REVERT: a 35 ASN cc_start: 0.9376 (m110) cc_final: 0.9092 (m-40) REVERT: a 57 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8400 (tt0) REVERT: b 174 MET cc_start: 0.7931 (tpp) cc_final: 0.7615 (tpp) REVERT: b 204 MET cc_start: 0.8837 (mtp) cc_final: 0.8399 (mmm) REVERT: c 315 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6232 (tp) REVERT: c 356 MET cc_start: 0.9017 (tpp) cc_final: 0.8399 (tpp) outliers start: 21 outliers final: 18 residues processed: 164 average time/residue: 0.2577 time to fit residues: 63.8587 Evaluate side-chains 161 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 175 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 216 HIS Chi-restraints excluded: chain c residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 12 optimal weight: 0.0050 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14619 Z= 0.202 Angle : 0.685 15.166 20112 Z= 0.352 Chirality : 0.041 0.306 2206 Planarity : 0.004 0.059 2263 Dihedral : 21.946 158.395 2641 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.57 % Allowed : 18.13 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.70 (0.22), residues: 1474 helix: 1.53 (0.19), residues: 769 sheet: 0.18 (0.48), residues: 111 loop : -0.89 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP a 226 HIS 0.003 0.001 HIS a 223 PHE 0.026 0.001 PHE M 304 TYR 0.021 0.001 TYR a 83 ARG 0.011 0.000 ARG V 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 221 ASN cc_start: 0.9223 (m-40) cc_final: 0.8786 (m110) REVERT: M 227 GLN cc_start: 0.9364 (mp10) cc_final: 0.9024 (mp10) REVERT: M 229 GLN cc_start: 0.9335 (tp40) cc_final: 0.9046 (tp40) REVERT: M 259 TYR cc_start: 0.9404 (t80) cc_final: 0.8908 (t80) REVERT: M 271 GLN cc_start: 0.9348 (mt0) cc_final: 0.8937 (mt0) REVERT: O 286 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7700 (tm-30) REVERT: O 295 MET cc_start: 0.8452 (ttm) cc_final: 0.8209 (ttm) REVERT: U 35 ASP cc_start: 0.8021 (p0) cc_final: 0.6980 (p0) REVERT: U 37 GLN cc_start: 0.9139 (mp-120) cc_final: 0.8616 (mp10) REVERT: U 355 ASP cc_start: 0.8350 (p0) cc_final: 0.8124 (p0) REVERT: V 27 GLN cc_start: 0.7130 (pp30) cc_final: 0.6722 (pp30) REVERT: V 35 GLN cc_start: 0.8896 (mp10) cc_final: 0.8539 (mp10) REVERT: V 50 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: V 89 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8810 (tptt) REVERT: a 35 ASN cc_start: 0.9389 (m110) cc_final: 0.9129 (m110) REVERT: a 57 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8406 (tt0) REVERT: b 174 MET cc_start: 0.7958 (tpp) cc_final: 0.7699 (tpp) REVERT: b 204 MET cc_start: 0.8846 (mtp) cc_final: 0.8319 (mmm) REVERT: c 142 MET cc_start: 0.8106 (tpp) cc_final: 0.7505 (mpp) REVERT: c 315 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6234 (tp) REVERT: c 356 MET cc_start: 0.9028 (tpp) cc_final: 0.8445 (tpp) outliers start: 21 outliers final: 18 residues processed: 164 average time/residue: 0.2679 time to fit residues: 67.6503 Evaluate side-chains 164 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 80 GLU Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 175 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 354 CYS Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 216 HIS Chi-restraints excluded: chain c residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 112 optimal weight: 0.0050 chunk 18 optimal weight: 0.0030 chunk 33 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 144 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.081550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.060599 restraints weight = 67571.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.062046 restraints weight = 32563.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.062898 restraints weight = 21187.256| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14619 Z= 0.186 Angle : 0.682 15.553 20112 Z= 0.350 Chirality : 0.041 0.308 2206 Planarity : 0.004 0.058 2263 Dihedral : 21.841 158.585 2641 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.65 % Allowed : 18.05 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.74 (0.22), residues: 1474 helix: 1.54 (0.19), residues: 768 sheet: 0.23 (0.48), residues: 111 loop : -0.84 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP a 226 HIS 0.003 0.000 HIS a 227 PHE 0.014 0.001 PHE U 351 TYR 0.023 0.001 TYR a 83 ARG 0.009 0.000 ARG d 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.16 seconds wall clock time: 53 minutes 3.76 seconds (3183.76 seconds total)