Starting phenix.real_space_refine on Sun Dec 29 14:11:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x2d_32965/12_2024/7x2d_32965.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x2d_32965/12_2024/7x2d_32965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x2d_32965/12_2024/7x2d_32965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x2d_32965/12_2024/7x2d_32965.map" model { file = "/net/cci-nas-00/data/ceres_data/7x2d_32965/12_2024/7x2d_32965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x2d_32965/12_2024/7x2d_32965.cif" } resolution = 3.3 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= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3052 atoms to isotropic. 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 C 5215 2.51 5 N 1428 2.21 5 O 1502 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8203 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 2241 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 280, 2230 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 280, 2230 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 bond proxies already assigned to first conformer: 2274 Chain: "A" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1883 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 2619 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Conformer: "B" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} bond proxies already assigned to first conformer: 2640 Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'86W': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS B 233 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 233 " occ=0.50 residue: pdb=" N ACYS B 271 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 271 " occ=0.50 Time building chain proxies: 7.22, per 1000 atoms: 0.88 Number of scatterers: 8203 At special positions: 0 Unit cell: (78.264, 97.83, 128.266, 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) S 55 16.00 F 3 9.00 O 1502 8.00 N 1428 7.00 C 5215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.04 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: 2.39 Conformation dependent library (CDL) restraints added in 1.4 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 44.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'F' and resid 20 through 51 removed outlier: 4.205A pdb=" N ILE F 24 " --> pdb=" O PHE F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 57 removed outlier: 3.980A pdb=" N ARG F 55 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS F 57 " --> pdb=" O HIS F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 77 removed outlier: 4.340A pdb=" N PHE F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL F 63 " --> pdb=" O THR F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 Processing helix chain 'F' and resid 94 through 127 removed outlier: 4.241A pdb=" N ILE F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA F 101 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 109 " --> pdb=" O MET F 105 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER F 127 " --> pdb=" O TRP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 135 removed outlier: 3.625A pdb=" N MET F 135 " --> pdb=" O TYR F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 161 removed outlier: 3.875A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 203 through 238 Processing helix chain 'F' and resid 265 through 298 removed outlier: 4.092A pdb=" N PHE F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL F 282 " --> pdb=" O MET F 278 " (cutoff:3.500A) Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 309 through 332 removed outlier: 4.798A pdb=" N SER F 324 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER F 325 " --> pdb=" O TRP F 321 " (cutoff:3.500A) Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 334 through 346 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.714A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.562A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.575A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.023A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.554A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 214 removed outlier: 9.237A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.685A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.756A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.969A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.694A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.839A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.441A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.789A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.764A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER E 59 " --> pdb=" O ASP E 50 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1223 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: 2.44 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1321 1.30 - 1.43: 2323 1.43 - 1.57: 4663 1.57 - 1.70: 0 1.70 - 1.83: 74 Bond restraints: 8381 Sorted by residual: bond pdb=" C19 86W F 502 " pdb=" C20 86W F 502 " ideal model delta sigma weight residual 1.359 1.479 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C24 86W F 502 " pdb=" N23 86W F 502 " ideal model delta sigma weight residual 1.372 1.465 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C24 86W F 502 " pdb=" N26 86W F 502 " ideal model delta sigma weight residual 1.380 1.467 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CA SER F 191 " pdb=" C SER F 191 " ideal model delta sigma weight residual 1.524 1.478 0.045 1.26e-02 6.30e+03 1.28e+01 bond pdb=" CA CYS F 186 " pdb=" C CYS F 186 " ideal model delta sigma weight residual 1.530 1.493 0.036 1.10e-02 8.26e+03 1.10e+01 ... (remaining 8376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 11169 2.82 - 5.64: 170 5.64 - 8.46: 25 8.46 - 11.28: 2 11.28 - 14.10: 1 Bond angle restraints: 11367 Sorted by residual: angle pdb=" N GLU D 42 " pdb=" CA GLU D 42 " pdb=" CB GLU D 42 " ideal model delta sigma weight residual 110.39 117.99 -7.60 1.66e+00 3.63e-01 2.09e+01 angle pdb=" C LYS A 233 " pdb=" N TRP A 234 " pdb=" CA TRP A 234 " ideal model delta sigma weight residual 121.94 112.86 9.08 2.00e+00 2.50e-01 2.06e+01 angle pdb=" N ILE F 125 " pdb=" CA ILE F 125 " pdb=" C ILE F 125 " ideal model delta sigma weight residual 113.53 109.20 4.33 9.80e-01 1.04e+00 1.95e+01 angle pdb=" C GLY A 353 " pdb=" N ASP A 354 " pdb=" CA ASP A 354 " ideal model delta sigma weight residual 122.07 128.37 -6.30 1.43e+00 4.89e-01 1.94e+01 angle pdb=" N ASN F 185 " pdb=" CA ASN F 185 " pdb=" C ASN F 185 " ideal model delta sigma weight residual 110.28 103.95 6.33 1.48e+00 4.57e-01 1.83e+01 ... (remaining 11362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4513 17.96 - 35.91: 420 35.91 - 53.87: 90 53.87 - 71.82: 11 71.82 - 89.78: 9 Dihedral angle restraints: 5043 sinusoidal: 2025 harmonic: 3018 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual 93.00 4.29 88.71 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS F 96 " pdb=" SG CYS F 96 " pdb=" SG CYS F 186 " pdb=" CB CYS F 186 " ideal model delta sinusoidal sigma weight residual 93.00 173.69 -80.69 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CA PHE F 333 " pdb=" C PHE F 333 " pdb=" N ASN F 334 " pdb=" CA ASN F 334 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 974 0.055 - 0.111: 245 0.111 - 0.166: 40 0.166 - 0.221: 11 0.221 - 0.277: 5 Chirality restraints: 1275 Sorted by residual: chirality pdb=" C13 CLR F 501 " pdb=" C12 CLR F 501 " pdb=" C14 CLR F 501 " pdb=" C17 CLR F 501 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA GLU D 42 " pdb=" N GLU D 42 " pdb=" C GLU D 42 " pdb=" CB GLU D 42 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ARG B 8 " pdb=" N ARG B 8 " pdb=" C ARG B 8 " pdb=" CB ARG B 8 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1272 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 157 " 0.081 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO F 158 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO F 158 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO F 158 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 169 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C TRP B 169 " 0.056 2.00e-02 2.50e+03 pdb=" O TRP B 169 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP B 170 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 28 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C LYS A 28 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS A 28 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 29 " -0.015 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 42 2.47 - 3.08: 5614 3.08 - 3.68: 12517 3.68 - 4.29: 18628 4.29 - 4.90: 31003 Nonbonded interactions: 67804 Sorted by model distance: nonbonded pdb=" F16 86W F 502 " pdb=" O08 86W F 502 " model vdw 1.860 2.990 nonbonded pdb=" OG1 THR F 37 " pdb=" OG SER F 325 " model vdw 2.078 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.079 3.040 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLN B 175 " model vdw 2.148 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.164 3.120 ... (remaining 67799 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=0.50 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.920 Find NCS groups from input model: 0.070 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 : 0.005 0.120 8381 Z= 0.343 Angle : 0.854 14.105 11367 Z= 0.474 Chirality : 0.053 0.277 1275 Planarity : 0.006 0.121 1440 Dihedral : 14.430 89.779 3076 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.57 % Allowed : 0.68 % Favored : 98.75 % Cbeta Deviations : 0.10 % 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: -0.46 (0.25), residues: 1021 helix: 0.60 (0.25), residues: 404 sheet: -0.57 (0.32), residues: 227 loop : -0.97 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 281 HIS 0.010 0.002 HIS A 220 PHE 0.032 0.002 PHE B 234 TYR 0.021 0.002 TYR A 253 ARG 0.006 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8926 (tp) cc_final: 0.8717 (tp) REVERT: F 157 ILE cc_start: 0.8838 (mm) cc_final: 0.8562 (mt) REVERT: A 386 MET cc_start: 0.7482 (ttp) cc_final: 0.7060 (ttm) REVERT: D 51 LEU cc_start: 0.7813 (tp) cc_final: 0.7431 (tp) REVERT: E 78 THR cc_start: 0.7646 (t) cc_final: 0.7315 (p) REVERT: E 117 TYR cc_start: 0.8412 (m-80) cc_final: 0.8179 (m-80) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.2089 time to fit residues: 54.3756 Evaluate side-chains 150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN A 292 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8381 Z= 0.261 Angle : 0.606 8.794 11367 Z= 0.327 Chirality : 0.044 0.136 1275 Planarity : 0.005 0.080 1440 Dihedral : 5.187 42.969 1216 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.48 % Allowed : 10.34 % Favored : 88.18 % 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 (0.25), residues: 1021 helix: 1.42 (0.24), residues: 409 sheet: 0.08 (0.33), residues: 218 loop : -0.67 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.007 0.001 HIS A 357 PHE 0.030 0.002 PHE F 141 TYR 0.014 0.002 TYR E 32 ARG 0.005 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8843 (tp) cc_final: 0.8620 (tp) REVERT: F 278 MET cc_start: 0.7469 (tpp) cc_final: 0.7088 (tpp) REVERT: A 307 LYS cc_start: 0.7282 (ptpp) cc_final: 0.6695 (pttp) REVERT: A 386 MET cc_start: 0.7558 (ttp) cc_final: 0.7211 (ttm) REVERT: B 197 ARG cc_start: 0.7717 (mmp80) cc_final: 0.7400 (mmp80) REVERT: B 325 MET cc_start: 0.7617 (mmm) cc_final: 0.7323 (tpp) outliers start: 10 outliers final: 9 residues processed: 160 average time/residue: 0.2100 time to fit residues: 46.6982 Evaluate side-chains 150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN E 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8381 Z= 0.317 Angle : 0.599 9.435 11367 Z= 0.321 Chirality : 0.044 0.138 1275 Planarity : 0.004 0.065 1440 Dihedral : 5.176 51.127 1216 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.18 % Allowed : 12.95 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1021 helix: 1.61 (0.24), residues: 417 sheet: -0.10 (0.32), residues: 227 loop : -0.42 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.002 PHE F 264 TYR 0.015 0.002 TYR B 105 ARG 0.007 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8857 (tp) cc_final: 0.8642 (tp) REVERT: F 333 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7230 (m-10) REVERT: A 307 LYS cc_start: 0.7468 (ptpp) cc_final: 0.6941 (pttp) REVERT: A 386 MET cc_start: 0.7537 (ttp) cc_final: 0.7137 (ttm) REVERT: B 197 ARG cc_start: 0.7759 (mmp80) cc_final: 0.7444 (mmp80) outliers start: 25 outliers final: 15 residues processed: 160 average time/residue: 0.2006 time to fit residues: 44.9165 Evaluate side-chains 154 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.0670 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8381 Z= 0.187 Angle : 0.522 7.631 11367 Z= 0.282 Chirality : 0.041 0.129 1275 Planarity : 0.004 0.057 1440 Dihedral : 4.903 49.553 1216 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.27 % Allowed : 14.32 % Favored : 83.41 % 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: 0.95 (0.26), residues: 1021 helix: 1.94 (0.25), residues: 417 sheet: 0.01 (0.32), residues: 219 loop : -0.38 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.009 0.001 HIS A 220 PHE 0.020 0.002 PHE B 253 TYR 0.014 0.001 TYR B 105 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8849 (tp) cc_final: 0.8641 (tp) REVERT: A 307 LYS cc_start: 0.7466 (ptpp) cc_final: 0.6942 (pttp) REVERT: A 386 MET cc_start: 0.7558 (ttp) cc_final: 0.7200 (ttm) REVERT: B 197 ARG cc_start: 0.7733 (mmp80) cc_final: 0.7455 (mmp-170) outliers start: 17 outliers final: 13 residues processed: 156 average time/residue: 0.1950 time to fit residues: 42.4529 Evaluate side-chains 150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8381 Z= 0.218 Angle : 0.527 7.031 11367 Z= 0.283 Chirality : 0.042 0.133 1275 Planarity : 0.004 0.053 1440 Dihedral : 4.863 50.659 1216 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.18 % Allowed : 14.55 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1021 helix: 2.12 (0.25), residues: 411 sheet: 0.06 (0.32), residues: 217 loop : -0.27 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 281 HIS 0.005 0.001 HIS A 220 PHE 0.020 0.002 PHE F 29 TYR 0.012 0.001 TYR B 105 ARG 0.002 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8856 (tp) cc_final: 0.8641 (tp) REVERT: F 278 MET cc_start: 0.7446 (mmm) cc_final: 0.7230 (tpp) REVERT: F 333 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7291 (m-10) REVERT: A 307 LYS cc_start: 0.7456 (ptpp) cc_final: 0.6982 (pttp) REVERT: A 386 MET cc_start: 0.7573 (ttp) cc_final: 0.7207 (ttm) REVERT: B 197 ARG cc_start: 0.7779 (mmp80) cc_final: 0.7454 (mmp80) REVERT: B 220 GLN cc_start: 0.7760 (mt0) cc_final: 0.7456 (mt0) outliers start: 25 outliers final: 19 residues processed: 154 average time/residue: 0.2148 time to fit residues: 45.9445 Evaluate side-chains 152 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 0.0060 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8381 Z= 0.181 Angle : 0.511 6.711 11367 Z= 0.273 Chirality : 0.041 0.132 1275 Planarity : 0.004 0.050 1440 Dihedral : 4.742 49.394 1216 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.07 % Allowed : 15.34 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1021 helix: 2.25 (0.25), residues: 411 sheet: 0.12 (0.32), residues: 217 loop : -0.24 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE F 264 TYR 0.010 0.001 TYR F 214 ARG 0.002 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8859 (tp) cc_final: 0.8645 (tp) REVERT: F 333 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7277 (m-10) REVERT: A 307 LYS cc_start: 0.7486 (ptpp) cc_final: 0.7030 (pttp) REVERT: A 386 MET cc_start: 0.7559 (ttp) cc_final: 0.7215 (ttm) REVERT: B 197 ARG cc_start: 0.7720 (mmp80) cc_final: 0.7415 (mmp80) REVERT: B 234 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7647 (t80) outliers start: 24 outliers final: 18 residues processed: 150 average time/residue: 0.2047 time to fit residues: 42.7827 Evaluate side-chains 150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8381 Z= 0.176 Angle : 0.501 6.669 11367 Z= 0.269 Chirality : 0.041 0.138 1275 Planarity : 0.003 0.047 1440 Dihedral : 4.632 47.636 1216 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.18 % Allowed : 15.80 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.27), residues: 1021 helix: 2.25 (0.25), residues: 417 sheet: 0.17 (0.32), residues: 218 loop : -0.15 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE F 29 TYR 0.008 0.001 TYR A 37 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8854 (tp) cc_final: 0.8645 (tp) REVERT: F 333 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7309 (m-10) REVERT: A 307 LYS cc_start: 0.7547 (ptpp) cc_final: 0.7036 (pttp) REVERT: A 386 MET cc_start: 0.7580 (ttp) cc_final: 0.7240 (ttm) REVERT: B 197 ARG cc_start: 0.7665 (mmp80) cc_final: 0.7428 (mmp80) REVERT: B 220 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: B 234 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7723 (t80) outliers start: 25 outliers final: 17 residues processed: 152 average time/residue: 0.1941 time to fit residues: 40.7460 Evaluate side-chains 152 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 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 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8381 Z= 0.165 Angle : 0.501 6.916 11367 Z= 0.268 Chirality : 0.041 0.127 1275 Planarity : 0.003 0.046 1440 Dihedral : 4.533 44.998 1216 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.95 % Allowed : 16.02 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.27), residues: 1021 helix: 2.32 (0.25), residues: 417 sheet: 0.25 (0.31), residues: 218 loop : -0.17 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE B 253 TYR 0.011 0.001 TYR E 117 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8848 (tp) cc_final: 0.8636 (tp) REVERT: F 333 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7371 (m-10) REVERT: A 307 LYS cc_start: 0.7514 (ptpp) cc_final: 0.7074 (pttt) REVERT: A 386 MET cc_start: 0.7577 (ttp) cc_final: 0.7251 (ttm) REVERT: B 220 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7266 (mt0) REVERT: B 234 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7703 (t80) outliers start: 23 outliers final: 18 residues processed: 148 average time/residue: 0.2152 time to fit residues: 43.9389 Evaluate side-chains 150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.3980 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.2980 chunk 84 optimal weight: 0.0980 chunk 89 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8381 Z= 0.138 Angle : 0.499 12.590 11367 Z= 0.262 Chirality : 0.040 0.130 1275 Planarity : 0.003 0.045 1440 Dihedral : 4.304 37.461 1216 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.93 % Allowed : 17.39 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 1021 helix: 2.47 (0.25), residues: 417 sheet: 0.29 (0.31), residues: 226 loop : -0.17 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 281 HIS 0.004 0.001 HIS A 220 PHE 0.022 0.001 PHE F 29 TYR 0.010 0.001 TYR E 117 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8849 (tp) cc_final: 0.8640 (tp) REVERT: F 278 MET cc_start: 0.7455 (mmm) cc_final: 0.7054 (tpp) REVERT: A 281 TRP cc_start: 0.8997 (m100) cc_final: 0.8745 (m100) REVERT: A 307 LYS cc_start: 0.7506 (ptpp) cc_final: 0.7076 (pttt) REVERT: A 386 MET cc_start: 0.7610 (ttp) cc_final: 0.7278 (ttm) REVERT: B 220 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7298 (mt0) REVERT: B 234 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7931 (t80) REVERT: B 331 SER cc_start: 0.9112 (t) cc_final: 0.8844 (p) outliers start: 14 outliers final: 10 residues processed: 148 average time/residue: 0.2108 time to fit residues: 43.0170 Evaluate side-chains 141 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 220 GLN D 44 HIS E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8381 Z= 0.337 Angle : 0.584 11.977 11367 Z= 0.310 Chirality : 0.044 0.229 1275 Planarity : 0.004 0.047 1440 Dihedral : 4.744 46.596 1216 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.27 % Allowed : 17.84 % Favored : 79.89 % 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: 1.30 (0.26), residues: 1021 helix: 2.34 (0.25), residues: 405 sheet: 0.10 (0.32), residues: 220 loop : -0.19 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 281 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.002 PHE F 264 TYR 0.021 0.002 TYR E 60 ARG 0.004 0.000 ARG E 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8895 (tp) cc_final: 0.8693 (tp) REVERT: F 278 MET cc_start: 0.7511 (mmm) cc_final: 0.7164 (tpp) REVERT: F 333 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: A 307 LYS cc_start: 0.7497 (ptpp) cc_final: 0.7066 (pttt) REVERT: A 386 MET cc_start: 0.7569 (ttp) cc_final: 0.7200 (ttm) REVERT: B 220 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: B 234 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.7754 (t80) REVERT: E 87 LYS cc_start: 0.7723 (mmtp) cc_final: 0.7287 (mptt) outliers start: 17 outliers final: 12 residues processed: 151 average time/residue: 0.2039 time to fit residues: 42.4297 Evaluate side-chains 150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.161745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.113865 restraints weight = 26088.584| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 4.53 r_work: 0.3016 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 8381 Z= 0.294 Angle : 1.023 59.200 11367 Z= 0.607 Chirality : 0.046 0.593 1275 Planarity : 0.005 0.112 1440 Dihedral : 4.756 46.899 1216 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.27 % Allowed : 17.61 % Favored : 80.11 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1021 helix: 2.37 (0.25), residues: 405 sheet: 0.01 (0.31), residues: 225 loop : -0.17 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 281 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.002 PHE F 264 TYR 0.017 0.002 TYR E 60 ARG 0.008 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2017.22 seconds wall clock time: 40 minutes 42.61 seconds (2442.61 seconds total)