Starting phenix.real_space_refine on Sat Apr 6 09:25:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/04_2024/8kh5_37237_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/04_2024/8kh5_37237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/04_2024/8kh5_37237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/04_2024/8kh5_37237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/04_2024/8kh5_37237_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/04_2024/8kh5_37237_updated.pdb" } resolution = 2.83 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= 0.003 sd= 0.143 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 P 1 5.49 5 S 57 5.16 5 C 5034 2.51 5 N 1339 2.21 5 O 1407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2214 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1778 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2460 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 116 Conformer: "B" Number of residues, atoms: 338, 2460 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 116 bond proxies already assigned to first conformer: 2496 Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 946 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 345 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'CLR': 2, 'LPS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.05, per 1000 atoms: 0.77 Number of scatterers: 7838 At special positions: 0 Unit cell: (74.52, 97.2, 130.68, 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 57 16.00 P 1 15.00 O 1407 8.00 N 1339 7.00 C 5034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 168 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.8 seconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 39.0% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 16 through 50 removed outlier: 4.321A pdb=" N VAL A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 81 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 88 through 121 removed outlier: 3.630A pdb=" N LYS A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 134 through 155 removed outlier: 3.526A pdb=" N CYS A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 179 through 212 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 224 through 257 removed outlier: 3.623A pdb=" N LEU A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Proline residue: A 245 - end of helix Proline residue: A 251 - end of helix Processing helix chain 'A' and resid 264 through 293 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'B' and resid 13 through 38 removed outlier: 3.595A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 308 through 311 No H-bonds generated for 'chain 'B' and resid 308 through 311' Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.651A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 392 removed outlier: 3.787A pdb=" N GLU B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'B' and resid 359 through 363 removed outlier: 7.189A pdb=" N VAL B 287 " --> pdb=" O TYR B 360 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N HIS B 362 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 289 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 243 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN B 218 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEU B 43 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS B 220 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU B 45 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE B 222 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.788A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.983A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.785A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.824A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.590A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.422A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.652A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.046A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1137 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: 2.79 Time building geometry restraints manager: 3.44 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: 1234 1.30 - 1.43: 2168 1.43 - 1.55: 4530 1.55 - 1.68: 4 1.68 - 1.81: 78 Bond restraints: 8014 Sorted by residual: bond pdb=" C PRO A 123 " pdb=" O PRO A 123 " ideal model delta sigma weight residual 1.237 1.410 -0.173 1.26e-02 6.30e+03 1.88e+02 bond pdb=" C31 LPS A 402 " pdb=" O32 LPS A 402 " ideal model delta sigma weight residual 1.398 1.180 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CA ALA A 140 " pdb=" C ALA A 140 " ideal model delta sigma weight residual 1.524 1.412 0.112 1.29e-02 6.01e+03 7.53e+01 bond pdb=" C ASP A 16 " pdb=" O ASP A 16 " ideal model delta sigma weight residual 1.235 1.314 -0.079 1.26e-02 6.30e+03 3.94e+01 bond pdb=" C PHE A 126 " pdb=" O PHE A 126 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.15e-02 7.56e+03 3.44e+01 ... (remaining 8009 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.44: 205 106.44 - 113.34: 4419 113.34 - 120.23: 2786 120.23 - 127.13: 3433 127.13 - 134.03: 84 Bond angle restraints: 10927 Sorted by residual: angle pdb=" N PHE A 126 " pdb=" CA PHE A 126 " pdb=" C PHE A 126 " ideal model delta sigma weight residual 111.07 123.34 -12.27 1.07e+00 8.73e-01 1.32e+02 angle pdb=" N CYS A 129 " pdb=" CA CYS A 129 " pdb=" C CYS A 129 " ideal model delta sigma weight residual 112.92 100.41 12.51 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N LYS A 130 " pdb=" CA LYS A 130 " pdb=" C LYS A 130 " ideal model delta sigma weight residual 112.57 102.29 10.28 1.13e+00 7.83e-01 8.28e+01 angle pdb=" CA PHE A 126 " pdb=" C PHE A 126 " pdb=" N HIS A 127 " ideal model delta sigma weight residual 117.07 126.17 -9.10 1.14e+00 7.69e-01 6.37e+01 angle pdb=" O PHE A 126 " pdb=" C PHE A 126 " pdb=" N HIS A 127 " ideal model delta sigma weight residual 122.07 114.52 7.55 1.03e+00 9.43e-01 5.37e+01 ... (remaining 10922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 4301 15.07 - 30.14: 382 30.14 - 45.21: 103 45.21 - 60.29: 19 60.29 - 75.36: 8 Dihedral angle restraints: 4813 sinusoidal: 1799 harmonic: 3014 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 147.71 -54.71 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" N PHE A 124 " pdb=" C PHE A 124 " pdb=" CA PHE A 124 " pdb=" CB PHE A 124 " ideal model delta harmonic sigma weight residual 122.80 110.88 11.92 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" CB CYS A 91 " pdb=" SG CYS A 91 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 131.85 -38.85 1 1.00e+01 1.00e-02 2.12e+01 ... (remaining 4810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.443: 1274 0.443 - 0.886: 1 0.886 - 1.329: 0 1.329 - 1.772: 0 1.772 - 2.214: 1 Chirality restraints: 1276 Sorted by residual: chirality pdb=" C31 LPS A 402 " pdb=" C32 LPS A 402 " pdb=" O31 LPS A 402 " pdb=" O32 LPS A 402 " both_signs ideal model delta sigma weight residual False -2.18 0.04 -2.21 2.00e-01 2.50e+01 1.23e+02 chirality pdb=" CA PHE A 126 " pdb=" N PHE A 126 " pdb=" C PHE A 126 " pdb=" CB PHE A 126 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.49e+00 chirality pdb=" C13 CLR A 401 " pdb=" C12 CLR A 401 " pdb=" C14 CLR A 401 " pdb=" C17 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 1273 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 124 " 0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C PHE A 124 " -0.085 2.00e-02 2.50e+03 pdb=" O PHE A 124 " 0.031 2.00e-02 2.50e+03 pdb=" N ARG A 125 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 126 " -0.025 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C PHE A 126 " 0.081 2.00e-02 2.50e+03 pdb=" O PHE A 126 " -0.028 2.00e-02 2.50e+03 pdb=" N HIS A 127 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 122 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 123 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.032 5.00e-02 4.00e+02 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 137 2.66 - 3.22: 7483 3.22 - 3.78: 12704 3.78 - 4.34: 17671 4.34 - 4.90: 29189 Nonbonded interactions: 67184 Sorted by model distance: nonbonded pdb=" OD1 ASP E 50 " pdb=" OG SER E 59 " model vdw 2.103 2.440 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.189 2.440 nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 171 " model vdw 2.197 2.440 nonbonded pdb=" NH1 ARG B 228 " pdb=" OD1 ASP C 186 " model vdw 2.249 2.520 nonbonded pdb=" O CYS C 149 " pdb=" NH1 ARG C 150 " model vdw 2.254 2.520 ... (remaining 67179 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=0.45 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: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.720 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.660 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.008 0.218 8014 Z= 0.535 Angle : 0.852 17.124 10927 Z= 0.505 Chirality : 0.084 2.214 1276 Planarity : 0.005 0.060 1371 Dihedral : 12.854 75.356 2856 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.26 % Allowed : 0.77 % Favored : 98.97 % 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: 0.90 (0.27), residues: 1018 helix: 1.86 (0.27), residues: 402 sheet: 0.40 (0.34), residues: 218 loop : -0.56 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 142 HIS 0.011 0.002 HIS C 142 PHE 0.028 0.002 PHE A 239 TYR 0.031 0.002 TYR C 59 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 118 TRP cc_start: 0.6917 (t-100) cc_final: 0.6332 (t60) REVERT: A 250 PHE cc_start: 0.7690 (t80) cc_final: 0.7479 (t80) REVERT: B 317 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7440 (mtm-85) REVERT: B 378 ASP cc_start: 0.7929 (m-30) cc_final: 0.7619 (m-30) REVERT: C 277 SER cc_start: 0.8496 (t) cc_final: 0.8110 (m) outliers start: 2 outliers final: 2 residues processed: 206 average time/residue: 1.1328 time to fit residues: 247.8046 Evaluate side-chains 134 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain B residue 229 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 0.0270 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 131 GLN B 23 ASN B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN C 119 ASN C 175 GLN C 176 GLN C 220 GLN C 259 GLN E 31 ASN D 44 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8014 Z= 0.269 Angle : 0.595 8.292 10927 Z= 0.312 Chirality : 0.044 0.151 1276 Planarity : 0.005 0.060 1371 Dihedral : 6.921 106.482 1276 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.22 % Allowed : 12.23 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.27), residues: 1018 helix: 2.00 (0.26), residues: 410 sheet: 0.39 (0.32), residues: 221 loop : -0.40 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.010 0.002 HIS B 220 PHE 0.027 0.002 PHE A 119 TYR 0.025 0.002 TYR C 59 ARG 0.009 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 118 TRP cc_start: 0.7543 (t-100) cc_final: 0.7227 (t-100) REVERT: A 185 MET cc_start: 0.7658 (tmm) cc_final: 0.7389 (tmm) REVERT: A 224 GLU cc_start: 0.7820 (mp0) cc_final: 0.7588 (mp0) REVERT: A 296 THR cc_start: 0.8563 (m) cc_final: 0.8132 (t) REVERT: A 300 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7871 (mtp180) REVERT: B 274 LYS cc_start: 0.7789 (tttt) cc_final: 0.7490 (ttpt) REVERT: B 310 ASP cc_start: 0.8039 (t0) cc_final: 0.7686 (m-30) REVERT: B 317 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7592 (mtm-85) REVERT: C 197 ARG cc_start: 0.7114 (mtp-110) cc_final: 0.6805 (mtp85) REVERT: C 214 ARG cc_start: 0.6603 (OUTLIER) cc_final: 0.6312 (mpp80) REVERT: C 275 SER cc_start: 0.8951 (p) cc_final: 0.8719 (m) REVERT: E 80 TYR cc_start: 0.7330 (m-80) cc_final: 0.6773 (m-80) REVERT: D 50 LEU cc_start: 0.7226 (mt) cc_final: 0.6989 (mt) outliers start: 25 outliers final: 11 residues processed: 158 average time/residue: 1.2164 time to fit residues: 203.3794 Evaluate side-chains 138 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 213 GLN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8014 Z= 0.206 Angle : 0.517 5.731 10927 Z= 0.275 Chirality : 0.042 0.144 1276 Planarity : 0.004 0.057 1371 Dihedral : 5.706 53.915 1272 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.70 % Allowed : 15.57 % Favored : 81.72 % 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: 1.22 (0.27), residues: 1018 helix: 2.23 (0.26), residues: 410 sheet: 0.27 (0.32), residues: 221 loop : -0.38 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.007 0.001 HIS B 357 PHE 0.026 0.002 PHE A 119 TYR 0.025 0.001 TYR C 59 ARG 0.007 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.901 Fit side-chains REVERT: A 92 MET cc_start: 0.6809 (tpt) cc_final: 0.6478 (mmp) REVERT: A 179 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7395 (tp) REVERT: A 185 MET cc_start: 0.7640 (tmm) cc_final: 0.7294 (tmm) REVERT: A 224 GLU cc_start: 0.7796 (mp0) cc_final: 0.7494 (mp0) REVERT: A 296 THR cc_start: 0.8567 (m) cc_final: 0.8052 (t) REVERT: A 300 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7773 (mtp180) REVERT: A 302 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7008 (ttm170) REVERT: B 274 LYS cc_start: 0.7829 (tttt) cc_final: 0.7518 (ttpt) REVERT: B 317 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7413 (ptp-110) REVERT: C 101 MET cc_start: 0.8930 (mtp) cc_final: 0.8642 (mtp) REVERT: C 197 ARG cc_start: 0.7146 (mtp-110) cc_final: 0.6689 (mtp85) REVERT: C 214 ARG cc_start: 0.6625 (mpp80) cc_final: 0.6272 (mpp80) REVERT: E 3 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7231 (mm-40) REVERT: E 80 TYR cc_start: 0.7451 (m-80) cc_final: 0.6822 (m-80) outliers start: 21 outliers final: 6 residues processed: 143 average time/residue: 1.3146 time to fit residues: 198.4482 Evaluate side-chains 125 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 0.0970 chunk 80 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 292 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 175 GLN C 220 GLN C 259 GLN E 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8014 Z= 0.269 Angle : 0.551 5.203 10927 Z= 0.292 Chirality : 0.043 0.149 1276 Planarity : 0.005 0.057 1371 Dihedral : 5.955 58.624 1272 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.22 % Allowed : 15.96 % Favored : 80.82 % 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: 1.19 (0.27), residues: 1018 helix: 2.21 (0.26), residues: 411 sheet: 0.25 (0.33), residues: 221 loop : -0.40 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.009 0.001 HIS B 357 PHE 0.028 0.002 PHE A 119 TYR 0.017 0.002 TYR C 59 ARG 0.008 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.7387 (mt) cc_final: 0.7103 (mt) REVERT: A 27 THR cc_start: 0.7800 (m) cc_final: 0.7583 (p) REVERT: A 92 MET cc_start: 0.7392 (tpt) cc_final: 0.7095 (mmp) REVERT: A 179 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7477 (tp) REVERT: A 188 ILE cc_start: 0.7277 (mt) cc_final: 0.7000 (mt) REVERT: A 296 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8108 (t) REVERT: A 300 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7710 (mtp180) REVERT: B 32 LYS cc_start: 0.8017 (ttmm) cc_final: 0.7644 (mttm) REVERT: B 211 LYS cc_start: 0.8654 (mttp) cc_final: 0.7790 (mmtm) REVERT: B 254 ASN cc_start: 0.8425 (m-40) cc_final: 0.8182 (t0) REVERT: B 274 LYS cc_start: 0.7846 (tttt) cc_final: 0.7523 (ttpt) REVERT: B 280 ARG cc_start: 0.7661 (ttt90) cc_final: 0.7426 (ttt-90) REVERT: B 317 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7449 (ptp-110) REVERT: C 55 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8378 (mt) REVERT: C 101 MET cc_start: 0.8944 (mtp) cc_final: 0.8708 (mtp) REVERT: C 197 ARG cc_start: 0.7219 (mtp-110) cc_final: 0.6691 (mtp85) REVERT: C 214 ARG cc_start: 0.6705 (mpp80) cc_final: 0.6433 (mpp80) REVERT: E 3 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7192 (mm-40) REVERT: E 83 MET cc_start: 0.8212 (mtp) cc_final: 0.7911 (mtp) outliers start: 25 outliers final: 9 residues processed: 162 average time/residue: 1.1657 time to fit residues: 200.5020 Evaluate side-chains 146 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0470 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 175 GLN C 220 GLN E 31 ASN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8014 Z= 0.173 Angle : 0.497 5.682 10927 Z= 0.261 Chirality : 0.041 0.140 1276 Planarity : 0.004 0.056 1371 Dihedral : 5.617 56.239 1272 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.09 % Allowed : 18.53 % Favored : 78.38 % 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 (0.27), residues: 1018 helix: 2.32 (0.26), residues: 410 sheet: 0.23 (0.32), residues: 227 loop : -0.32 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.005 0.001 HIS B 220 PHE 0.026 0.001 PHE A 119 TYR 0.011 0.001 TYR A 79 ARG 0.007 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.306 Fit side-chains REVERT: A 21 ILE cc_start: 0.7277 (mt) cc_final: 0.7066 (mt) REVERT: A 27 THR cc_start: 0.7752 (m) cc_final: 0.7520 (p) REVERT: A 92 MET cc_start: 0.7492 (tpt) cc_final: 0.7227 (mmp) REVERT: A 179 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7493 (tp) REVERT: A 185 MET cc_start: 0.7709 (tmm) cc_final: 0.7347 (tmm) REVERT: A 188 ILE cc_start: 0.7135 (mt) cc_final: 0.6829 (mt) REVERT: A 296 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8096 (p) REVERT: A 300 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7718 (mtp180) REVERT: B 32 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7625 (mttm) REVERT: B 213 GLN cc_start: 0.8961 (tt0) cc_final: 0.8733 (tt0) REVERT: B 239 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8515 (p0) REVERT: B 274 LYS cc_start: 0.7829 (tttt) cc_final: 0.7511 (ttpt) REVERT: B 317 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7540 (ptp-110) REVERT: B 318 TYR cc_start: 0.8363 (t80) cc_final: 0.8016 (t80) REVERT: C 55 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8327 (mt) REVERT: C 101 MET cc_start: 0.8959 (mtp) cc_final: 0.8630 (mtp) REVERT: C 197 ARG cc_start: 0.7191 (mtp-110) cc_final: 0.6727 (mtp85) REVERT: C 214 ARG cc_start: 0.6699 (mpp80) cc_final: 0.6447 (mpp80) outliers start: 24 outliers final: 8 residues processed: 152 average time/residue: 1.1546 time to fit residues: 186.8887 Evaluate side-chains 146 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8014 Z= 0.247 Angle : 0.530 6.530 10927 Z= 0.278 Chirality : 0.043 0.147 1276 Planarity : 0.004 0.056 1371 Dihedral : 5.577 44.447 1272 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.35 % Allowed : 17.76 % Favored : 78.89 % 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: 1.21 (0.27), residues: 1018 helix: 2.23 (0.26), residues: 409 sheet: 0.14 (0.33), residues: 221 loop : -0.29 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.007 0.001 HIS B 357 PHE 0.027 0.002 PHE A 119 TYR 0.012 0.002 TYR E 95 ARG 0.010 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 0.897 Fit side-chains REVERT: A 21 ILE cc_start: 0.7325 (mt) cc_final: 0.7068 (mt) REVERT: A 92 MET cc_start: 0.7697 (tpt) cc_final: 0.7489 (mmp) REVERT: A 185 MET cc_start: 0.7715 (tmm) cc_final: 0.7358 (tmm) REVERT: A 300 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7727 (mtp180) REVERT: B 25 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7752 (tttt) REVERT: B 32 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7701 (mttm) REVERT: B 213 GLN cc_start: 0.8899 (tt0) cc_final: 0.8643 (tt0) REVERT: B 239 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8582 (p0) REVERT: B 274 LYS cc_start: 0.7841 (tttt) cc_final: 0.7507 (ttpt) REVERT: B 317 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7528 (ptp-110) REVERT: C 55 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8391 (mt) REVERT: C 101 MET cc_start: 0.8924 (mtp) cc_final: 0.8717 (mtp) REVERT: C 137 ARG cc_start: 0.7285 (mtp-110) cc_final: 0.7052 (ttm-80) REVERT: E 83 MET cc_start: 0.8043 (mtp) cc_final: 0.7774 (mtm) outliers start: 26 outliers final: 13 residues processed: 148 average time/residue: 1.1214 time to fit residues: 176.7824 Evaluate side-chains 146 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8014 Z= 0.204 Angle : 0.515 7.960 10927 Z= 0.266 Chirality : 0.041 0.141 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.365 43.746 1272 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.96 % Allowed : 19.05 % Favored : 77.99 % 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: 1.21 (0.26), residues: 1018 helix: 2.28 (0.26), residues: 407 sheet: 0.21 (0.33), residues: 214 loop : -0.37 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS B 357 PHE 0.026 0.002 PHE A 119 TYR 0.010 0.001 TYR E 95 ARG 0.010 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 0.901 Fit side-chains REVERT: A 21 ILE cc_start: 0.7280 (mt) cc_final: 0.7038 (mt) REVERT: A 296 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8084 (p) REVERT: A 300 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7678 (mtp180) REVERT: B 25 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7779 (tttt) REVERT: B 32 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7654 (mttm) REVERT: B 213 GLN cc_start: 0.8804 (tt0) cc_final: 0.8556 (tm-30) REVERT: B 239 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8593 (p0) REVERT: B 274 LYS cc_start: 0.7853 (tttt) cc_final: 0.7520 (ttpt) REVERT: B 317 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7576 (ptp-110) REVERT: C 55 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8369 (mt) REVERT: C 101 MET cc_start: 0.8911 (mtp) cc_final: 0.8699 (mtp) REVERT: C 197 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.6983 (mtp85) REVERT: E 80 TYR cc_start: 0.7718 (m-80) cc_final: 0.7299 (m-80) REVERT: E 83 MET cc_start: 0.8074 (mtp) cc_final: 0.7752 (mtp) outliers start: 23 outliers final: 11 residues processed: 149 average time/residue: 1.0950 time to fit residues: 173.9156 Evaluate side-chains 146 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 292 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8014 Z= 0.205 Angle : 0.514 9.282 10927 Z= 0.267 Chirality : 0.041 0.141 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.394 43.297 1272 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.09 % Allowed : 19.69 % Favored : 77.22 % 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: 1.22 (0.27), residues: 1018 helix: 2.27 (0.26), residues: 409 sheet: 0.12 (0.33), residues: 216 loop : -0.30 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS B 357 PHE 0.028 0.002 PHE A 77 TYR 0.012 0.001 TYR A 22 ARG 0.010 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.995 Fit side-chains REVERT: A 21 ILE cc_start: 0.7261 (mt) cc_final: 0.7028 (mt) REVERT: A 296 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 300 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7655 (mtp180) REVERT: B 32 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7555 (mttm) REVERT: B 213 GLN cc_start: 0.8796 (tt0) cc_final: 0.8561 (tm-30) REVERT: B 274 LYS cc_start: 0.7842 (tttt) cc_final: 0.7501 (ttpt) REVERT: B 317 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7604 (ptp-110) REVERT: C 55 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8368 (mt) REVERT: C 101 MET cc_start: 0.8917 (mtp) cc_final: 0.8679 (mtp) REVERT: C 137 ARG cc_start: 0.7154 (mtp-110) cc_final: 0.6771 (ttt90) REVERT: C 197 ARG cc_start: 0.7402 (ttm-80) cc_final: 0.6743 (mtp85) REVERT: E 80 TYR cc_start: 0.7753 (m-80) cc_final: 0.7326 (m-80) REVERT: E 83 MET cc_start: 0.8058 (mtp) cc_final: 0.7649 (mtp) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 1.1621 time to fit residues: 180.4697 Evaluate side-chains 144 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 292 ASN B 294 GLN C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8014 Z= 0.194 Angle : 0.519 7.219 10927 Z= 0.268 Chirality : 0.041 0.140 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.350 43.564 1272 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.70 % Allowed : 20.59 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1018 helix: 2.26 (0.26), residues: 407 sheet: 0.16 (0.32), residues: 214 loop : -0.36 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS B 357 PHE 0.026 0.001 PHE A 119 TYR 0.010 0.001 TYR B 391 ARG 0.010 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 0.943 Fit side-chains REVERT: A 21 ILE cc_start: 0.7248 (mt) cc_final: 0.7016 (mt) REVERT: A 296 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8093 (p) REVERT: B 25 LYS cc_start: 0.8026 (ttpp) cc_final: 0.7764 (tttt) REVERT: B 32 LYS cc_start: 0.7942 (ttmm) cc_final: 0.7560 (mttm) REVERT: B 213 GLN cc_start: 0.8752 (tt0) cc_final: 0.8535 (tm-30) REVERT: B 274 LYS cc_start: 0.7853 (tttt) cc_final: 0.7518 (ttpt) REVERT: B 317 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7616 (ptp-110) REVERT: C 55 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8358 (mt) REVERT: C 137 ARG cc_start: 0.7153 (mtp-110) cc_final: 0.6697 (ttm-80) REVERT: E 80 TYR cc_start: 0.7760 (m-80) cc_final: 0.7307 (m-80) REVERT: E 83 MET cc_start: 0.8056 (mtp) cc_final: 0.7663 (mtp) outliers start: 21 outliers final: 13 residues processed: 145 average time/residue: 1.2002 time to fit residues: 184.8984 Evaluate side-chains 144 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.0570 chunk 99 optimal weight: 0.0050 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.0970 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.2910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8014 Z= 0.158 Angle : 0.505 7.857 10927 Z= 0.257 Chirality : 0.040 0.135 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.098 44.440 1272 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.16 % Allowed : 22.52 % Favored : 76.32 % 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: 1.31 (0.27), residues: 1018 helix: 2.32 (0.26), residues: 409 sheet: 0.25 (0.32), residues: 230 loop : -0.30 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.005 0.001 HIS B 220 PHE 0.041 0.001 PHE A 77 TYR 0.016 0.001 TYR A 22 ARG 0.009 0.000 ARG C 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 0.984 Fit side-chains REVERT: A 296 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8060 (p) REVERT: A 301 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.6868 (mtm-85) REVERT: B 32 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7658 (mttm) REVERT: B 213 GLN cc_start: 0.8562 (tt0) cc_final: 0.8315 (tm-30) REVERT: B 274 LYS cc_start: 0.7833 (tttt) cc_final: 0.7497 (ttpt) REVERT: B 317 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7630 (ptp-110) REVERT: C 137 ARG cc_start: 0.7068 (mtp-110) cc_final: 0.6773 (ttm-80) REVERT: C 214 ARG cc_start: 0.7017 (mpp80) cc_final: 0.6807 (mpp80) REVERT: E 80 TYR cc_start: 0.7639 (m-80) cc_final: 0.7126 (m-80) REVERT: E 83 MET cc_start: 0.8052 (mtp) cc_final: 0.7757 (mtp) outliers start: 9 outliers final: 4 residues processed: 149 average time/residue: 1.1871 time to fit residues: 188.6071 Evaluate side-chains 136 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122748 restraints weight = 17246.382| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.03 r_work: 0.3281 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8014 Z= 0.190 Angle : 0.511 8.379 10927 Z= 0.263 Chirality : 0.041 0.135 1276 Planarity : 0.004 0.054 1371 Dihedral : 5.191 44.494 1272 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.29 % Allowed : 23.29 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.27), residues: 1018 helix: 2.39 (0.26), residues: 406 sheet: 0.27 (0.32), residues: 230 loop : -0.23 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS B 357 PHE 0.025 0.001 PHE A 119 TYR 0.014 0.001 TYR A 78 ARG 0.009 0.000 ARG C 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.86 seconds wall clock time: 63 minutes 9.48 seconds (3789.48 seconds total)