Starting phenix.real_space_refine on Fri Nov 15 12:47:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgt_60090/11_2024/8zgt_60090.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgt_60090/11_2024/8zgt_60090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgt_60090/11_2024/8zgt_60090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgt_60090/11_2024/8zgt_60090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgt_60090/11_2024/8zgt_60090.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgt_60090/11_2024/8zgt_60090.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5713 2.51 5 N 1483 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8915 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1729 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 4, 'TRANS': 207} Chain: "B" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1227 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 1, 'TRANS': 156} Chain: "C" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2602 Classifications: {'peptide': 320} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 300} Chain: "F" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2571 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 295} Chain: "G" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 274 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.85, per 1000 atoms: 0.66 Number of scatterers: 8915 At special positions: 0 Unit cell: (80.75, 103.55, 169.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1679 8.00 N 1483 7.00 C 5713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 91 " distance=2.04 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 171 " distance=2.04 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS G 25 " distance=2.03 Simple disulfide: pdb=" SG CYS E 112 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 184 " distance=2.04 Simple disulfide: pdb=" SG CYS E 230 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 334 " - pdb=" SG CYS E 396 " distance=2.04 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 184 " distance=2.04 Simple disulfide: pdb=" SG CYS F 230 " - pdb=" SG CYS F 289 " distance=2.03 Simple disulfide: pdb=" SG CYS F 334 " - pdb=" SG CYS F 396 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 301 " - " ASN A 158 " " NAG A 302 " - " ASN A 167 " " NAG D 1 " - " ASN E 265 " " NAG E 501 " - " ASN E 240 " " NAG E 502 " - " ASN E 170 " " NAG F 501 " - " ASN F 170 " " NAG H 1 " - " ASN F 265 " " NAG T 1 " - " ASN A 65 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 991.2 milliseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 20 sheets defined 29.3% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.544A pdb=" N SER A 86 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.570A pdb=" N SER A 169 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.603A pdb=" N GLN A 204 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 236 removed outlier: 3.892A pdb=" N ILE A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.538A pdb=" N LYS B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 56' Processing helix chain 'B' and resid 58 through 83 removed outlier: 3.977A pdb=" N GLN B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 78 " --> pdb=" O CYS B 74 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 79 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.562A pdb=" N PHE B 88 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 99 through 122 removed outlier: 3.575A pdb=" N TRP B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 160 removed outlier: 3.619A pdb=" N ALA B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 207 removed outlier: 3.505A pdb=" N PHE B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU B 187 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 58 removed outlier: 4.199A pdb=" N ALA C 30 " --> pdb=" O TYR C 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 31 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 216 through 222 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.744A pdb=" N TRP E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.804A pdb=" N HIS E 360 " --> pdb=" O LYS E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'F' and resid 173 through 177 Processing helix chain 'F' and resid 204 through 208 Processing helix chain 'F' and resid 216 through 222 Processing helix chain 'F' and resid 277 through 284 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 385 through 389 Processing helix chain 'G' and resid 25 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 64 Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 115 removed outlier: 3.540A pdb=" N ILE A 128 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 119 through 121 removed outlier: 6.433A pdb=" N VAL A 120 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR A 177 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS A 140 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 151 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS A 145 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ALA A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 119 through 121 removed outlier: 6.433A pdb=" N VAL A 120 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 104 through 109 removed outlier: 5.310A pdb=" N ALA E 163 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS E 157 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR E 166 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU E 155 " --> pdb=" O TYR E 166 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG E 168 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN E 153 " --> pdb=" O ARG E 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 144 through 145 Processing sheet with id=AA9, first strand: chain 'E' and resid 209 through 213 removed outlier: 3.946A pdb=" N THR E 229 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP E 234 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR E 268 " --> pdb=" O ASP E 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 242 through 246 Processing sheet with id=AB2, first strand: chain 'E' and resid 315 through 319 removed outlier: 3.843A pdb=" N THR E 333 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE E 375 " --> pdb=" O ASN E 338 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 315 through 319 removed outlier: 3.843A pdb=" N THR E 333 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE E 375 " --> pdb=" O ASN E 338 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG E 374 " --> pdb=" O TYR E 368 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 345 through 350 Processing sheet with id=AB5, first strand: chain 'F' and resid 104 through 109 removed outlier: 4.958A pdb=" N ALA F 163 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU F 162 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLU F 158 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER F 164 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 144 through 145 removed outlier: 3.527A pdb=" N ALA F 195 " --> pdb=" O CYS F 184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 209 through 213 removed outlier: 3.916A pdb=" N ASP F 234 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR F 268 " --> pdb=" O ASP F 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 242 through 246 Processing sheet with id=AB9, first strand: chain 'F' and resid 315 through 319 removed outlier: 3.864A pdb=" N THR F 333 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE F 375 " --> pdb=" O ASN F 338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 315 through 319 removed outlier: 3.864A pdb=" N THR F 333 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE F 375 " --> pdb=" O ASN F 338 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 366 " --> pdb=" O PHE F 376 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 345 through 350 removed outlier: 3.522A pdb=" N SER F 345 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR F 395 " --> pdb=" O LEU F 349 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1200 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: 2.68 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2304 1.33 - 1.46: 2315 1.46 - 1.58: 4453 1.58 - 1.71: 0 1.71 - 1.84: 49 Bond restraints: 9121 Sorted by residual: bond pdb=" N GLU A 199 " pdb=" CA GLU A 199 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.15e-02 7.56e+03 7.88e+00 bond pdb=" C1 NAG F 501 " pdb=" O5 NAG F 501 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.93e+00 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" C1 NAG E 502 " pdb=" O5 NAG E 502 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.42e+00 ... (remaining 9116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 12208 2.83 - 5.65: 150 5.65 - 8.48: 21 8.48 - 11.31: 2 11.31 - 14.13: 2 Bond angle restraints: 12383 Sorted by residual: angle pdb=" C ASP F 134 " pdb=" N VAL F 135 " pdb=" CA VAL F 135 " ideal model delta sigma weight residual 121.97 133.57 -11.60 1.80e+00 3.09e-01 4.15e+01 angle pdb=" C TYR F 368 " pdb=" N ASN F 369 " pdb=" CA ASN F 369 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C GLN F 390 " pdb=" N THR F 391 " pdb=" CA THR F 391 " ideal model delta sigma weight residual 122.46 128.96 -6.50 1.41e+00 5.03e-01 2.13e+01 angle pdb=" C GLN E 390 " pdb=" N THR E 391 " pdb=" CA THR E 391 " ideal model delta sigma weight residual 122.82 128.62 -5.80 1.42e+00 4.96e-01 1.67e+01 angle pdb=" CA LEU B 110 " pdb=" CB LEU B 110 " pdb=" CG LEU B 110 " ideal model delta sigma weight residual 116.30 130.43 -14.13 3.50e+00 8.16e-02 1.63e+01 ... (remaining 12378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 5022 21.62 - 43.25: 545 43.25 - 64.87: 112 64.87 - 86.50: 28 86.50 - 108.12: 9 Dihedral angle restraints: 5716 sinusoidal: 2532 harmonic: 3184 Sorted by residual: dihedral pdb=" CA ILE A 198 " pdb=" C ILE A 198 " pdb=" N GLU A 199 " pdb=" CA GLU A 199 " ideal model delta harmonic sigma weight residual 180.00 138.76 41.24 0 5.00e+00 4.00e-02 6.80e+01 dihedral pdb=" CA ASP A 33 " pdb=" C ASP A 33 " pdb=" N PRO A 34 " pdb=" CA PRO A 34 " ideal model delta harmonic sigma weight residual 180.00 151.06 28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA TYR F 368 " pdb=" C TYR F 368 " pdb=" N ASN F 369 " pdb=" CA ASN F 369 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1098 0.053 - 0.105: 273 0.105 - 0.158: 71 0.158 - 0.210: 7 0.210 - 0.263: 4 Chirality restraints: 1453 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ASN F 369 " pdb=" N ASN F 369 " pdb=" C ASN F 369 " pdb=" CB ASN F 369 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1450 not shown) Planarity restraints: 1527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 198 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.90e+01 pdb=" C ILE A 198 " -0.093 2.00e-02 2.50e+03 pdb=" O ILE A 198 " 0.035 2.00e-02 2.50e+03 pdb=" N GLU A 199 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 320 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO F 321 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO F 321 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 321 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 113 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO E 114 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " 0.030 5.00e-02 4.00e+02 ... (remaining 1524 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1579 2.78 - 3.31: 7156 3.31 - 3.84: 13991 3.84 - 4.37: 15781 4.37 - 4.90: 28932 Nonbonded interactions: 67439 Sorted by model distance: nonbonded pdb=" OG1 THR A 25 " pdb=" OE1 GLN A 26 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR A 25 " pdb=" N GLN A 26 " model vdw 2.320 3.120 nonbonded pdb=" OD1 ASN E 265 " pdb=" OG1 THR E 267 " model vdw 2.330 3.040 nonbonded pdb=" O THR E 225 " pdb=" OG1 THR E 225 " model vdw 2.332 3.040 nonbonded pdb=" O ASP E 142 " pdb=" O6 NAG D 1 " model vdw 2.350 3.040 ... (remaining 67434 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 Found NCS groups: ncs_group { reference = (chain 'C' and resid 24 through 57) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 101 through 416 or resid 502)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.570 Find NCS groups from input model: 0.250 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:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9121 Z= 0.267 Angle : 0.789 14.135 12383 Z= 0.413 Chirality : 0.052 0.263 1453 Planarity : 0.006 0.066 1519 Dihedral : 18.714 108.121 3613 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 4.14 % Allowed : 25.63 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), residues: 1065 helix: -1.11 (0.26), residues: 272 sheet: 1.08 (0.28), residues: 337 loop : -1.23 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 PHE 0.018 0.002 PHE F 339 TYR 0.016 0.001 TYR A 103 ARG 0.017 0.001 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 38 residues processed: 125 average time/residue: 0.8971 time to fit residues: 122.9614 Evaluate side-chains 123 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN E 393 GLN F 189 GLN F 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9121 Z= 0.204 Angle : 0.584 7.523 12383 Z= 0.309 Chirality : 0.045 0.156 1453 Planarity : 0.004 0.038 1519 Dihedral : 11.490 75.603 1559 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 4.24 % Allowed : 25.23 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % 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: 0.20 (0.25), residues: 1065 helix: 0.48 (0.31), residues: 261 sheet: 1.39 (0.28), residues: 342 loop : -1.06 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.006 0.001 HIS A 173 PHE 0.017 0.002 PHE E 339 TYR 0.016 0.001 TYR A 172 ARG 0.006 0.000 ARG F 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 1.107 Fit side-chains REVERT: A 186 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: E 369 ASN cc_start: 0.7897 (t160) cc_final: 0.7577 (t0) outliers start: 42 outliers final: 24 residues processed: 124 average time/residue: 0.9758 time to fit residues: 132.1919 Evaluate side-chains 110 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 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 204 GLN E 152 GLN ** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9121 Z= 0.189 Angle : 0.555 7.348 12383 Z= 0.292 Chirality : 0.045 0.174 1453 Planarity : 0.004 0.031 1519 Dihedral : 9.790 65.065 1522 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 4.74 % Allowed : 24.62 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1065 helix: 1.18 (0.31), residues: 267 sheet: 1.36 (0.27), residues: 358 loop : -1.02 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.005 0.001 HIS A 173 PHE 0.015 0.002 PHE E 339 TYR 0.015 0.001 TYR B 158 ARG 0.004 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 94 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 186 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8196 (m-30) REVERT: A 221 LEU cc_start: 0.4441 (OUTLIER) cc_final: 0.3674 (mp) REVERT: F 165 THR cc_start: 0.7934 (t) cc_final: 0.7661 (m) REVERT: F 338 ASN cc_start: 0.8292 (t0) cc_final: 0.8048 (t0) outliers start: 47 outliers final: 25 residues processed: 130 average time/residue: 0.8444 time to fit residues: 121.0722 Evaluate side-chains 111 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 64 optimal weight: 0.0970 chunk 95 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS E 152 GLN E 223 ASN E 369 ASN ** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9121 Z= 0.178 Angle : 0.544 8.125 12383 Z= 0.285 Chirality : 0.044 0.175 1453 Planarity : 0.003 0.029 1519 Dihedral : 8.980 59.387 1521 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 4.54 % Allowed : 24.82 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % 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: 0.75 (0.25), residues: 1065 helix: 1.52 (0.31), residues: 268 sheet: 1.40 (0.27), residues: 358 loop : -0.95 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 PHE 0.013 0.001 PHE F 126 TYR 0.011 0.001 TYR A 172 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8388 (t0) REVERT: A 186 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: A 221 LEU cc_start: 0.4451 (OUTLIER) cc_final: 0.3685 (mp) REVERT: E 213 ILE cc_start: 0.8372 (pt) cc_final: 0.8141 (mt) REVERT: F 338 ASN cc_start: 0.8284 (t0) cc_final: 0.7972 (t0) outliers start: 45 outliers final: 28 residues processed: 128 average time/residue: 0.8601 time to fit residues: 121.2709 Evaluate side-chains 114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN E 347 GLN ** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9121 Z= 0.180 Angle : 0.545 8.755 12383 Z= 0.285 Chirality : 0.044 0.170 1453 Planarity : 0.003 0.029 1519 Dihedral : 8.639 59.076 1520 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 3.94 % Allowed : 25.23 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % 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: 0.83 (0.25), residues: 1065 helix: 1.68 (0.32), residues: 268 sheet: 1.43 (0.27), residues: 358 loop : -0.95 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.005 0.001 HIS A 173 PHE 0.013 0.001 PHE E 339 TYR 0.015 0.001 TYR B 158 ARG 0.004 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8373 (t0) REVERT: A 186 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8148 (m-30) REVERT: A 221 LEU cc_start: 0.4456 (OUTLIER) cc_final: 0.3682 (mp) REVERT: B 167 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: E 213 ILE cc_start: 0.8320 (pt) cc_final: 0.8118 (mt) REVERT: F 338 ASN cc_start: 0.8291 (t0) cc_final: 0.7952 (t0) outliers start: 39 outliers final: 25 residues processed: 119 average time/residue: 0.9364 time to fit residues: 123.3775 Evaluate side-chains 113 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN E 223 ASN F 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9121 Z= 0.232 Angle : 0.580 9.111 12383 Z= 0.301 Chirality : 0.046 0.171 1453 Planarity : 0.004 0.034 1519 Dihedral : 8.602 58.796 1516 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 4.24 % Allowed : 24.82 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % 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: 0.81 (0.25), residues: 1065 helix: 1.67 (0.31), residues: 268 sheet: 1.44 (0.27), residues: 358 loop : -0.99 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.006 0.001 HIS A 173 PHE 0.018 0.002 PHE E 339 TYR 0.012 0.001 TYR A 144 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 90 time to evaluate : 1.044 Fit side-chains REVERT: A 105 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8324 (t0) REVERT: A 186 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: A 221 LEU cc_start: 0.4636 (OUTLIER) cc_final: 0.3835 (mp) REVERT: B 167 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: F 338 ASN cc_start: 0.8360 (t0) cc_final: 0.8006 (t0) outliers start: 42 outliers final: 29 residues processed: 125 average time/residue: 0.8930 time to fit residues: 122.4495 Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.0170 chunk 101 optimal weight: 0.0000 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.0010 overall best weight: 0.2230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS B 151 ASN E 223 ASN E 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9121 Z= 0.133 Angle : 0.555 12.268 12383 Z= 0.282 Chirality : 0.050 0.866 1453 Planarity : 0.003 0.029 1519 Dihedral : 7.728 58.219 1516 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 3.03 % Allowed : 26.34 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1065 helix: 1.89 (0.31), residues: 268 sheet: 1.43 (0.27), residues: 358 loop : -0.84 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.003 0.000 HIS A 173 PHE 0.011 0.001 PHE F 376 TYR 0.013 0.001 TYR B 158 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 1.128 Fit side-chains REVERT: A 163 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7880 (mttt) REVERT: A 186 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: B 167 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: E 369 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7635 (t0) REVERT: F 122 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8345 (tp40) REVERT: F 131 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6865 (mm) REVERT: F 338 ASN cc_start: 0.8271 (t0) cc_final: 0.7931 (t0) outliers start: 30 outliers final: 19 residues processed: 109 average time/residue: 0.9682 time to fit residues: 115.6329 Evaluate side-chains 109 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain F residue 122 GLN Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9121 Z= 0.165 Angle : 0.545 10.026 12383 Z= 0.280 Chirality : 0.047 0.604 1453 Planarity : 0.003 0.029 1519 Dihedral : 7.429 58.149 1514 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.40 % Rotamer: Outliers : 2.93 % Allowed : 26.64 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1065 helix: 1.90 (0.31), residues: 268 sheet: 1.45 (0.27), residues: 358 loop : -0.85 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.003 0.001 HIS A 173 PHE 0.012 0.001 PHE F 126 TYR 0.012 0.001 TYR F 124 ARG 0.006 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.977 Fit side-chains REVERT: A 105 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8301 (t0) REVERT: A 163 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7872 (mttt) REVERT: A 186 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: A 221 LEU cc_start: 0.4616 (OUTLIER) cc_final: 0.3857 (mp) REVERT: B 167 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: F 131 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6885 (mm) REVERT: F 338 ASN cc_start: 0.8297 (t0) cc_final: 0.7934 (t0) outliers start: 29 outliers final: 21 residues processed: 109 average time/residue: 1.0230 time to fit residues: 121.2073 Evaluate side-chains 110 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.0070 chunk 61 optimal weight: 0.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9121 Z= 0.155 Angle : 0.547 10.071 12383 Z= 0.282 Chirality : 0.047 0.672 1453 Planarity : 0.003 0.030 1519 Dihedral : 7.404 59.241 1514 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 3.13 % Allowed : 26.74 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1065 helix: 1.95 (0.31), residues: 268 sheet: 1.45 (0.27), residues: 358 loop : -0.82 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.003 0.001 HIS A 173 PHE 0.012 0.001 PHE F 126 TYR 0.016 0.001 TYR B 158 ARG 0.008 0.000 ARG F 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 1.117 Fit side-chains REVERT: A 163 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7959 (mttt) REVERT: A 186 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: B 167 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: F 131 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7061 (mm) REVERT: F 238 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7279 (tt0) REVERT: F 338 ASN cc_start: 0.8286 (t0) cc_final: 0.7946 (t0) outliers start: 31 outliers final: 23 residues processed: 107 average time/residue: 0.9896 time to fit residues: 115.3634 Evaluate side-chains 110 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.0980 chunk 104 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 ASN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9121 Z= 0.179 Angle : 0.564 9.996 12383 Z= 0.292 Chirality : 0.047 0.595 1453 Planarity : 0.003 0.032 1519 Dihedral : 7.333 57.421 1514 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 3.23 % Allowed : 26.74 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % 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: 1.04 (0.25), residues: 1065 helix: 1.98 (0.31), residues: 267 sheet: 1.47 (0.27), residues: 358 loop : -0.82 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.003 0.001 HIS A 173 PHE 0.012 0.001 PHE E 339 TYR 0.014 0.001 TYR F 124 ARG 0.008 0.000 ARG F 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 1.200 Fit side-chains REVERT: A 163 LYS cc_start: 0.8251 (ttmm) cc_final: 0.7956 (mttt) REVERT: A 186 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: B 167 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: E 369 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7647 (t0) REVERT: F 131 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.7002 (mm) REVERT: F 238 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7337 (tt0) REVERT: F 338 ASN cc_start: 0.8315 (t0) cc_final: 0.7942 (t0) outliers start: 32 outliers final: 23 residues processed: 113 average time/residue: 0.9656 time to fit residues: 120.3506 Evaluate side-chains 112 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN E 223 ASN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.187696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134011 restraints weight = 9916.349| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.85 r_work: 0.3328 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9121 Z= 0.209 Angle : 0.582 9.962 12383 Z= 0.301 Chirality : 0.050 0.799 1453 Planarity : 0.004 0.031 1519 Dihedral : 7.471 57.370 1514 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 3.03 % Allowed : 26.84 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % 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: 1.01 (0.25), residues: 1065 helix: 1.94 (0.31), residues: 267 sheet: 1.47 (0.27), residues: 358 loop : -0.86 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.003 0.001 HIS E 360 PHE 0.015 0.001 PHE E 339 TYR 0.017 0.001 TYR B 158 ARG 0.008 0.000 ARG F 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3009.57 seconds wall clock time: 55 minutes 5.27 seconds (3305.27 seconds total)