Starting phenix.real_space_refine on Sat Apr 6 12:09:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8j_36951/04_2024/8k8j_36951_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8j_36951/04_2024/8k8j_36951.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8j_36951/04_2024/8k8j_36951_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8j_36951/04_2024/8k8j_36951_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8j_36951/04_2024/8k8j_36951_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8j_36951/04_2024/8k8j_36951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8j_36951/04_2024/8k8j_36951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8j_36951/04_2024/8k8j_36951_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8j_36951/04_2024/8k8j_36951_neut_updated.pdb" } resolution = 2.88 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= 0.002 sd= 1.030 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: 5 Type Number sf(0) Gaussians S 55 5.16 5 Cl 1 4.86 5 C 5184 2.51 5 N 1418 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8155 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1970 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 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: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 372 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2227 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'J3O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.51, per 1000 atoms: 0.55 Number of scatterers: 8155 At special positions: 0 Unit cell: (72.384, 102.336, 133.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 55 16.00 O 1497 8.00 N 1418 7.00 C 5184 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 257 " - pdb=" SG CYS R 264 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 38.9% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 10 through 37 removed outlier: 3.665A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.671A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.906A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 380 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.724A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'G' and resid 7 through 19 Processing helix chain 'G' and resid 28 through 41 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 113 through 143 Processing helix chain 'R' and resid 145 through 149 Processing helix chain 'R' and resid 151 through 178 removed outlier: 4.298A pdb=" N ILE R 175 " --> pdb=" O VAL R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 219 removed outlier: 3.578A pdb=" N LEU R 190 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE R 191 " --> pdb=" O ASN R 187 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER R 199 " --> pdb=" O GLY R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 227 No H-bonds generated for 'chain 'R' and resid 224 through 227' Processing helix chain 'R' and resid 230 through 253 Proline residue: R 251 - end of helix Processing helix chain 'R' and resid 273 through 303 Processing helix chain 'R' and resid 306 through 309 No H-bonds generated for 'chain 'R' and resid 306 through 309' Processing helix chain 'R' and resid 339 through 367 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 373 through 397 removed outlier: 4.104A pdb=" N VAL R 378 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA R 380 " --> pdb=" O LYS R 376 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE R 381 " --> pdb=" O THR R 377 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS R 386 " --> pdb=" O CYS R 382 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU R 387 " --> pdb=" O SER R 383 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 402 through 410 Processing sheet with id= A, first strand: chain 'A' and resid 349 through 353 removed outlier: 7.307A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.744A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.925A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.587A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.095A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.582A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 93 through 98 removed outlier: 6.237A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1107 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: 2.29 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1358 1.32 - 1.44: 2243 1.44 - 1.57: 4636 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8316 Sorted by residual: bond pdb=" C4 J3O R 501 " pdb=" O1 J3O R 501 " ideal model delta sigma weight residual 1.400 1.327 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C2 J3O R 501 " pdb=" O1 J3O R 501 " ideal model delta sigma weight residual 1.402 1.464 -0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" C16 J3O R 501 " pdb="CL1 J3O R 501 " ideal model delta sigma weight residual 1.786 1.737 0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C5 J3O R 501 " pdb=" O3 J3O R 501 " ideal model delta sigma weight residual 1.402 1.448 -0.046 2.00e-02 2.50e+03 5.39e+00 bond pdb=" C12 J3O R 501 " pdb=" C13 J3O R 501 " ideal model delta sigma weight residual 1.533 1.489 0.044 2.00e-02 2.50e+03 4.85e+00 ... (remaining 8311 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.79: 110 105.79 - 112.87: 4531 112.87 - 119.94: 2763 119.94 - 127.01: 3763 127.01 - 134.09: 91 Bond angle restraints: 11258 Sorted by residual: angle pdb=" C PHE R 108 " pdb=" CA PHE R 108 " pdb=" CB PHE R 108 " ideal model delta sigma weight residual 111.22 101.84 9.38 1.24e+00 6.50e-01 5.72e+01 angle pdb=" C12 J3O R 501 " pdb=" C11 J3O R 501 " pdb=" C19 J3O R 501 " ideal model delta sigma weight residual 97.66 114.65 -16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" C10 J3O R 501 " pdb=" C11 J3O R 501 " pdb=" C12 J3O R 501 " ideal model delta sigma weight residual 140.96 126.82 14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C5 J3O R 501 " pdb=" O3 J3O R 501 " pdb=" C8 J3O R 501 " ideal model delta sigma weight residual 113.91 123.62 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CA PHE R 108 " pdb=" C PHE R 108 " pdb=" O PHE R 108 " ideal model delta sigma weight residual 120.37 115.87 4.50 1.56e+00 4.11e-01 8.31e+00 ... (remaining 11253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 4475 17.48 - 34.95: 403 34.95 - 52.43: 52 52.43 - 69.91: 17 69.91 - 87.39: 13 Dihedral angle restraints: 4960 sinusoidal: 1962 harmonic: 2998 Sorted by residual: dihedral pdb=" CB CYS R 257 " pdb=" SG CYS R 257 " pdb=" SG CYS R 264 " pdb=" CB CYS R 264 " ideal model delta sinusoidal sigma weight residual -86.00 -27.77 -58.23 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CA MET G 21 " pdb=" C MET G 21 " pdb=" N GLU G 22 " pdb=" CA GLU G 22 " ideal model delta harmonic sigma weight residual 180.00 161.01 18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 870 0.039 - 0.078: 302 0.078 - 0.117: 90 0.117 - 0.156: 15 0.156 - 0.195: 2 Chirality restraints: 1279 Sorted by residual: chirality pdb=" CG LEU B 210 " pdb=" CB LEU B 210 " pdb=" CD1 LEU B 210 " pdb=" CD2 LEU B 210 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA PHE R 108 " pdb=" N PHE R 108 " pdb=" C PHE R 108 " pdb=" CB PHE R 108 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA TRP B 339 " pdb=" N TRP B 339 " pdb=" C TRP B 339 " pdb=" CB TRP B 339 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 1276 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 J3O R 501 " -0.021 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C12 J3O R 501 " 0.066 2.00e-02 2.50e+03 pdb=" C13 J3O R 501 " -0.021 2.00e-02 2.50e+03 pdb=" O4 J3O R 501 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 J3O R 501 " 0.023 2.00e-02 2.50e+03 2.19e-02 9.60e+00 pdb=" C11 J3O R 501 " -0.049 2.00e-02 2.50e+03 pdb=" C12 J3O R 501 " 0.019 2.00e-02 2.50e+03 pdb=" C19 J3O R 501 " 0.005 2.00e-02 2.50e+03 pdb=" C20 J3O R 501 " 0.001 2.00e-02 2.50e+03 pdb=" C8 J3O R 501 " 0.018 2.00e-02 2.50e+03 pdb=" C9 J3O R 501 " -0.015 2.00e-02 2.50e+03 pdb=" O3 J3O R 501 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO B 236 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 531 2.73 - 3.27: 8404 3.27 - 3.82: 13883 3.82 - 4.36: 17127 4.36 - 4.90: 29498 Nonbonded interactions: 69443 Sorted by model distance: nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.190 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.204 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.221 2.440 nonbonded pdb=" OG1 THR N 28 " pdb=" OD1 ASN N 31 " model vdw 2.222 2.440 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.233 2.440 ... (remaining 69438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.010 Extract box with map and model: 7.110 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.230 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.004 0.073 8316 Z= 0.257 Angle : 0.611 16.985 11258 Z= 0.317 Chirality : 0.043 0.195 1279 Planarity : 0.003 0.050 1426 Dihedral : 14.020 87.387 3011 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.11 % Allowed : 0.45 % Favored : 99.44 % 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: 0.30 (0.26), residues: 1017 helix: 1.67 (0.26), residues: 380 sheet: -0.35 (0.34), residues: 229 loop : -0.83 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 339 HIS 0.004 0.001 HIS A 347 PHE 0.028 0.002 PHE R 177 TYR 0.011 0.001 TYR R 153 ARG 0.002 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 0.903 Fit side-chains REVERT: B 78 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8409 (tppp) REVERT: B 118 ASP cc_start: 0.8597 (p0) cc_final: 0.8340 (p0) REVERT: B 258 ASP cc_start: 0.7745 (t0) cc_final: 0.7408 (t0) REVERT: G 32 LYS cc_start: 0.7511 (tmmt) cc_final: 0.7268 (tttt) REVERT: R 129 PHE cc_start: 0.7164 (m-10) cc_final: 0.6918 (m-10) outliers start: 1 outliers final: 1 residues processed: 156 average time/residue: 1.4046 time to fit residues: 230.7254 Evaluate side-chains 122 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.0000 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.0870 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.0470 chunk 89 optimal weight: 0.8980 overall best weight: 0.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 375 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN R 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8316 Z= 0.152 Angle : 0.503 10.452 11258 Z= 0.262 Chirality : 0.040 0.133 1279 Planarity : 0.003 0.052 1426 Dihedral : 5.625 79.589 1131 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.35 % Allowed : 10.82 % Favored : 87.82 % 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: 0.47 (0.27), residues: 1017 helix: 1.90 (0.27), residues: 386 sheet: -0.32 (0.34), residues: 227 loop : -0.84 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.002 0.001 HIS A 347 PHE 0.016 0.001 PHE R 189 TYR 0.020 0.001 TYR R 153 ARG 0.005 0.000 ARG R 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.877 Fit side-chains REVERT: A 31 GLN cc_start: 0.7533 (tp40) cc_final: 0.7248 (mp10) REVERT: B 105 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8523 (t80) REVERT: B 118 ASP cc_start: 0.8551 (p0) cc_final: 0.8289 (p0) REVERT: B 186 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: B 195 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7559 (p0) REVERT: B 246 ASP cc_start: 0.8487 (m-30) cc_final: 0.8280 (m-30) REVERT: B 258 ASP cc_start: 0.7624 (t0) cc_final: 0.7302 (t0) REVERT: R 129 PHE cc_start: 0.7158 (m-10) cc_final: 0.6939 (m-10) outliers start: 12 outliers final: 5 residues processed: 138 average time/residue: 1.2650 time to fit residues: 184.8299 Evaluate side-chains 126 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 411 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.0870 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN R 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8316 Z= 0.150 Angle : 0.474 9.556 11258 Z= 0.249 Chirality : 0.040 0.132 1279 Planarity : 0.003 0.046 1426 Dihedral : 5.015 72.234 1129 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.92 % Allowed : 13.19 % Favored : 84.89 % 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: 0.58 (0.27), residues: 1017 helix: 2.00 (0.27), residues: 390 sheet: -0.33 (0.33), residues: 227 loop : -0.77 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 339 HIS 0.003 0.000 HIS A 347 PHE 0.012 0.001 PHE A 212 TYR 0.012 0.001 TYR R 153 ARG 0.003 0.000 ARG R 186 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 0.941 Fit side-chains REVERT: A 31 GLN cc_start: 0.7505 (tp40) cc_final: 0.7215 (mp10) REVERT: B 105 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8671 (t80) REVERT: B 118 ASP cc_start: 0.8547 (p0) cc_final: 0.8290 (p0) REVERT: B 186 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7060 (m-30) REVERT: B 195 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7579 (p0) REVERT: B 228 ASP cc_start: 0.8601 (p0) cc_final: 0.8172 (p0) REVERT: B 246 ASP cc_start: 0.8467 (m-30) cc_final: 0.8210 (m-30) REVERT: B 258 ASP cc_start: 0.7595 (t0) cc_final: 0.7241 (t0) REVERT: G 17 GLU cc_start: 0.7680 (tp30) cc_final: 0.7339 (mm-30) REVERT: R 354 ILE cc_start: 0.8186 (tp) cc_final: 0.7881 (tt) outliers start: 17 outliers final: 11 residues processed: 142 average time/residue: 1.2671 time to fit residues: 190.9637 Evaluate side-chains 135 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 411 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8316 Z= 0.204 Angle : 0.503 9.902 11258 Z= 0.264 Chirality : 0.041 0.136 1279 Planarity : 0.003 0.045 1426 Dihedral : 5.118 65.259 1129 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.80 % Allowed : 15.56 % Favored : 82.64 % 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: 0.55 (0.27), residues: 1017 helix: 1.97 (0.26), residues: 390 sheet: -0.33 (0.33), residues: 227 loop : -0.80 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.001 PHE N 108 TYR 0.016 0.001 TYR R 153 ARG 0.002 0.000 ARG R 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 0.965 Fit side-chains REVERT: A 31 GLN cc_start: 0.7544 (tp40) cc_final: 0.7249 (mp10) REVERT: A 213 GLN cc_start: 0.8232 (mt0) cc_final: 0.8008 (tt0) REVERT: B 46 ARG cc_start: 0.7818 (tpm170) cc_final: 0.7559 (tpp-160) REVERT: B 105 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8771 (t80) REVERT: B 118 ASP cc_start: 0.8538 (p0) cc_final: 0.8289 (p0) REVERT: B 186 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7068 (m-30) REVERT: B 195 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7542 (p0) REVERT: B 246 ASP cc_start: 0.8516 (m-30) cc_final: 0.8247 (m-30) REVERT: B 258 ASP cc_start: 0.7602 (t0) cc_final: 0.7277 (t0) outliers start: 16 outliers final: 12 residues processed: 140 average time/residue: 1.2926 time to fit residues: 191.8781 Evaluate side-chains 139 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 411 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN R 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8316 Z= 0.182 Angle : 0.492 9.917 11258 Z= 0.259 Chirality : 0.040 0.157 1279 Planarity : 0.003 0.045 1426 Dihedral : 4.946 62.476 1129 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.82 % Allowed : 16.69 % Favored : 80.50 % 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: 0.59 (0.27), residues: 1017 helix: 2.00 (0.26), residues: 390 sheet: -0.32 (0.33), residues: 233 loop : -0.76 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.013 0.001 TYR R 153 ARG 0.002 0.000 ARG R 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 0.934 Fit side-chains REVERT: A 20 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7053 (ttp-110) REVERT: A 31 GLN cc_start: 0.7537 (tp40) cc_final: 0.7241 (mp10) REVERT: A 213 GLN cc_start: 0.8266 (mt0) cc_final: 0.8026 (tt0) REVERT: B 46 ARG cc_start: 0.7821 (tpm170) cc_final: 0.7579 (tpp-160) REVERT: B 70 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8739 (pt) REVERT: B 118 ASP cc_start: 0.8533 (p0) cc_final: 0.8281 (p0) REVERT: B 186 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: B 195 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7539 (p0) REVERT: B 228 ASP cc_start: 0.8568 (p0) cc_final: 0.8019 (p0) REVERT: B 246 ASP cc_start: 0.8517 (m-30) cc_final: 0.8172 (m-30) REVERT: B 258 ASP cc_start: 0.7561 (t0) cc_final: 0.7210 (t0) REVERT: R 284 SER cc_start: 0.8211 (m) cc_final: 0.7732 (p) outliers start: 25 outliers final: 13 residues processed: 151 average time/residue: 1.2080 time to fit residues: 193.5820 Evaluate side-chains 142 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 401 SER Chi-restraints excluded: chain R residue 411 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 79 optimal weight: 0.0470 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8316 Z= 0.164 Angle : 0.504 9.470 11258 Z= 0.263 Chirality : 0.040 0.135 1279 Planarity : 0.003 0.043 1426 Dihedral : 4.786 55.536 1129 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.48 % Allowed : 18.04 % Favored : 79.48 % 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: 0.62 (0.27), residues: 1017 helix: 2.04 (0.26), residues: 390 sheet: -0.33 (0.33), residues: 233 loop : -0.75 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.011 0.001 TYR R 153 ARG 0.002 0.000 ARG R 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.063 Fit side-chains REVERT: A 19 GLN cc_start: 0.8343 (tt0) cc_final: 0.8051 (tt0) REVERT: A 31 GLN cc_start: 0.7523 (tp40) cc_final: 0.7221 (mp10) REVERT: B 46 ARG cc_start: 0.7856 (tpm170) cc_final: 0.7610 (tpp-160) REVERT: B 70 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8734 (pt) REVERT: B 118 ASP cc_start: 0.8545 (p0) cc_final: 0.8285 (p0) REVERT: B 186 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.6928 (m-30) REVERT: B 195 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7539 (p0) REVERT: B 228 ASP cc_start: 0.8588 (p0) cc_final: 0.7927 (p0) REVERT: B 246 ASP cc_start: 0.8561 (m-30) cc_final: 0.8221 (m-30) REVERT: B 258 ASP cc_start: 0.7570 (t0) cc_final: 0.7193 (t0) REVERT: R 354 ILE cc_start: 0.8172 (tp) cc_final: 0.7857 (tt) REVERT: R 401 SER cc_start: 0.7026 (OUTLIER) cc_final: 0.6576 (p) REVERT: R 402 LYS cc_start: 0.7073 (mtpt) cc_final: 0.6652 (mttp) outliers start: 22 outliers final: 13 residues processed: 148 average time/residue: 1.2192 time to fit residues: 191.6629 Evaluate side-chains 147 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 401 SER Chi-restraints excluded: chain R residue 411 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN R 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8316 Z= 0.190 Angle : 0.506 8.982 11258 Z= 0.266 Chirality : 0.040 0.134 1279 Planarity : 0.003 0.043 1426 Dihedral : 4.769 51.082 1129 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.93 % Allowed : 18.04 % Favored : 79.03 % 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: 0.62 (0.27), residues: 1017 helix: 2.02 (0.26), residues: 392 sheet: -0.32 (0.33), residues: 233 loop : -0.75 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 PHE 0.012 0.001 PHE A 212 TYR 0.013 0.001 TYR R 153 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.961 Fit side-chains REVERT: A 20 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7060 (ttp-110) REVERT: A 28 LYS cc_start: 0.8214 (mmtp) cc_final: 0.7481 (ptmm) REVERT: A 31 GLN cc_start: 0.7543 (tp40) cc_final: 0.7244 (mp10) REVERT: B 46 ARG cc_start: 0.7853 (tpm170) cc_final: 0.7607 (tpp-160) REVERT: B 70 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8735 (pt) REVERT: B 118 ASP cc_start: 0.8531 (p0) cc_final: 0.8280 (p0) REVERT: B 186 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: B 195 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7539 (p0) REVERT: B 226 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7757 (mt-10) REVERT: B 228 ASP cc_start: 0.8599 (p0) cc_final: 0.7993 (p0) REVERT: B 246 ASP cc_start: 0.8573 (m-30) cc_final: 0.8303 (m-30) REVERT: B 258 ASP cc_start: 0.7604 (t0) cc_final: 0.7267 (t0) REVERT: R 276 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7760 (mt) REVERT: R 284 SER cc_start: 0.8215 (m) cc_final: 0.7742 (p) REVERT: R 401 SER cc_start: 0.6926 (OUTLIER) cc_final: 0.6510 (p) REVERT: R 402 LYS cc_start: 0.7028 (mtpt) cc_final: 0.6612 (mttp) outliers start: 26 outliers final: 15 residues processed: 148 average time/residue: 1.1961 time to fit residues: 188.0599 Evaluate side-chains 152 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 401 SER Chi-restraints excluded: chain R residue 411 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 0.0170 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8316 Z= 0.206 Angle : 0.525 8.855 11258 Z= 0.274 Chirality : 0.041 0.134 1279 Planarity : 0.003 0.043 1426 Dihedral : 4.769 50.310 1129 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.82 % Allowed : 18.71 % Favored : 78.47 % 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: 0.59 (0.26), residues: 1017 helix: 1.96 (0.26), residues: 392 sheet: -0.31 (0.33), residues: 231 loop : -0.74 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.004 0.001 HIS A 347 PHE 0.013 0.001 PHE A 212 TYR 0.013 0.001 TYR R 153 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.896 Fit side-chains REVERT: A 20 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7059 (ttp-110) REVERT: A 28 LYS cc_start: 0.8235 (mmtp) cc_final: 0.7501 (ptmm) REVERT: A 31 GLN cc_start: 0.7553 (tp40) cc_final: 0.7257 (mp10) REVERT: B 46 ARG cc_start: 0.7910 (tpm170) cc_final: 0.7637 (tpp-160) REVERT: B 70 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8738 (pt) REVERT: B 118 ASP cc_start: 0.8530 (p0) cc_final: 0.8281 (p0) REVERT: B 186 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.6942 (m-30) REVERT: B 195 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7533 (p0) REVERT: B 226 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7799 (mt-10) REVERT: B 246 ASP cc_start: 0.8613 (m-30) cc_final: 0.8350 (m-30) REVERT: B 258 ASP cc_start: 0.7639 (t0) cc_final: 0.7327 (t0) REVERT: R 284 SER cc_start: 0.8236 (m) cc_final: 0.7758 (p) REVERT: R 401 SER cc_start: 0.6951 (OUTLIER) cc_final: 0.6516 (p) REVERT: R 402 LYS cc_start: 0.7036 (mtpt) cc_final: 0.6693 (mttp) outliers start: 25 outliers final: 17 residues processed: 148 average time/residue: 1.2126 time to fit residues: 190.8214 Evaluate side-chains 148 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 401 SER Chi-restraints excluded: chain R residue 411 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 175 GLN R 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8316 Z= 0.261 Angle : 0.546 9.267 11258 Z= 0.288 Chirality : 0.042 0.139 1279 Planarity : 0.003 0.043 1426 Dihedral : 4.990 55.401 1129 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.71 % Allowed : 19.28 % Favored : 78.02 % 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: 0.48 (0.26), residues: 1017 helix: 1.83 (0.26), residues: 392 sheet: -0.28 (0.33), residues: 233 loop : -0.81 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.004 0.001 HIS A 347 PHE 0.017 0.002 PHE N 108 TYR 0.016 0.001 TYR R 153 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7065 (ttp-110) REVERT: A 28 LYS cc_start: 0.8246 (mmtp) cc_final: 0.7501 (ptmm) REVERT: A 31 GLN cc_start: 0.7620 (tp40) cc_final: 0.7330 (mp10) REVERT: B 46 ARG cc_start: 0.7872 (tpm170) cc_final: 0.7605 (tpp-160) REVERT: B 70 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8748 (pt) REVERT: B 118 ASP cc_start: 0.8518 (p0) cc_final: 0.8270 (p0) REVERT: B 186 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: B 195 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7513 (p0) REVERT: B 246 ASP cc_start: 0.8608 (m-30) cc_final: 0.8296 (m-30) REVERT: B 258 ASP cc_start: 0.7633 (t0) cc_final: 0.7335 (t0) REVERT: R 129 PHE cc_start: 0.7138 (m-10) cc_final: 0.6864 (m-10) REVERT: R 276 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7582 (mt) REVERT: R 284 SER cc_start: 0.8192 (m) cc_final: 0.7699 (p) REVERT: R 401 SER cc_start: 0.7007 (OUTLIER) cc_final: 0.6551 (p) outliers start: 24 outliers final: 14 residues processed: 139 average time/residue: 1.2665 time to fit residues: 187.0232 Evaluate side-chains 143 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 401 SER Chi-restraints excluded: chain R residue 411 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0970 chunk 65 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 175 GLN R 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8316 Z= 0.178 Angle : 0.513 8.746 11258 Z= 0.269 Chirality : 0.040 0.135 1279 Planarity : 0.003 0.043 1426 Dihedral : 4.707 47.571 1129 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.03 % Allowed : 20.18 % Favored : 77.79 % 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: 0.67 (0.27), residues: 1017 helix: 2.09 (0.26), residues: 384 sheet: -0.22 (0.33), residues: 229 loop : -0.74 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR R 153 ARG 0.005 0.000 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.939 Fit side-chains REVERT: A 28 LYS cc_start: 0.8233 (mmtp) cc_final: 0.7506 (ptmm) REVERT: A 31 GLN cc_start: 0.7537 (tp40) cc_final: 0.7243 (mp10) REVERT: B 46 ARG cc_start: 0.7883 (tpm170) cc_final: 0.7631 (tpp-160) REVERT: B 118 ASP cc_start: 0.8536 (p0) cc_final: 0.8290 (p0) REVERT: B 186 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: B 226 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7703 (mt-10) REVERT: B 246 ASP cc_start: 0.8593 (m-30) cc_final: 0.8342 (m-30) REVERT: B 258 ASP cc_start: 0.7578 (t0) cc_final: 0.7174 (t0) REVERT: R 129 PHE cc_start: 0.7158 (m-10) cc_final: 0.6877 (m-10) REVERT: R 276 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7778 (mt) REVERT: R 284 SER cc_start: 0.8223 (m) cc_final: 0.7746 (p) REVERT: R 402 LYS cc_start: 0.7137 (mtpt) cc_final: 0.6598 (mttp) outliers start: 18 outliers final: 14 residues processed: 139 average time/residue: 1.2452 time to fit residues: 183.8902 Evaluate side-chains 141 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 411 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.136024 restraints weight = 9385.513| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.21 r_work: 0.3442 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8316 Z= 0.197 Angle : 0.533 8.517 11258 Z= 0.277 Chirality : 0.041 0.142 1279 Planarity : 0.003 0.043 1426 Dihedral : 4.674 45.696 1129 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.92 % Allowed : 20.29 % Favored : 77.79 % 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: 0.65 (0.27), residues: 1017 helix: 2.09 (0.26), residues: 384 sheet: -0.29 (0.33), residues: 231 loop : -0.73 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.003 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR R 153 ARG 0.005 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.98 seconds wall clock time: 65 minutes 4.82 seconds (3904.82 seconds total)