Starting phenix.real_space_refine on Tue Apr 29 22:28:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7t_36941/04_2025/8k7t_36941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7t_36941/04_2025/8k7t_36941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k7t_36941/04_2025/8k7t_36941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7t_36941/04_2025/8k7t_36941.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7t_36941/04_2025/8k7t_36941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7t_36941/04_2025/8k7t_36941.cif" } resolution = 3.71 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= 0.001 sd= 0.124 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 43 5.16 5 C 5722 2.51 5 N 1451 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1743 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 208} Chain: "G" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "H" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 341 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "E" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2511 Classifications: {'peptide': 315} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 294} Chain: "F" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2511 Classifications: {'peptide': 315} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 294} Chain: "C" 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: "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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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: 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 Time building chain proxies: 5.24, per 1000 atoms: 0.59 Number of scatterers: 8948 At special positions: 0 Unit cell: (87.15, 102.09, 163.095, 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 43 16.00 O 1732 8.00 N 1451 7.00 C 5722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS H 25 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 180 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 226 " - pdb=" SG CYS E 285 " distance=2.04 Simple disulfide: pdb=" SG CYS E 330 " - pdb=" SG CYS E 392 " distance=2.03 Simple disulfide: pdb=" SG CYS F 121 " - pdb=" SG CYS F 180 " distance=2.04 Simple disulfide: pdb=" SG CYS F 226 " - pdb=" SG CYS F 285 " distance=2.03 Simple disulfide: pdb=" SG CYS F 330 " - pdb=" SG CYS F 392 " distance=2.03 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 301 " - " ASN A 73 " " NAG A 302 " - " ASN A 167 " " NAG A 303 " - " ASN A 152 " " NAG C 1 " - " ASN A 66 " " NAG D 1 " - " ASN A 106 " " NAG E 501 " - " ASN E 238 " " NAG E 502 " - " ASN E 166 " " NAG F 501 " - " ASN F 166 " " NAG F 502 " - " ASN F 238 " " NAG I 1 " - " ASN E 261 " " NAG J 1 " - " ASN F 261 " Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 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: 18 helices and 19 sheets defined 28.9% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.834A pdb=" N LEU A 55 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN A 56 " --> pdb=" O ASN A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 56' Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.539A pdb=" N GLN A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 236 Processing helix chain 'G' and resid 23 through 58 Processing helix chain 'H' and resid 21 through 62 removed outlier: 3.947A pdb=" N CYS H 25 " --> pdb=" O GLU H 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 75 removed outlier: 5.183A pdb=" N LYS B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LYS B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 removed outlier: 3.680A pdb=" N ARG B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 154 removed outlier: 4.041A pdb=" N GLY B 121 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 199 Processing helix chain 'E' and resid 168 through 174 removed outlier: 3.588A pdb=" N SER E 174 " --> pdb=" O GLN E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 218 Processing helix chain 'E' and resid 273 through 280 removed outlier: 3.858A pdb=" N TRP E 277 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 278 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 212 through 218 Processing helix chain 'F' and resid 273 through 280 removed outlier: 3.942A pdb=" N TRP F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 386 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.839A pdb=" N ILE A 39 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121 removed outlier: 4.507A pdb=" N TYR A 177 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LYS A 141 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 142 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR A 153 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR A 144 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.682A pdb=" N GLY A 125 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE A 127 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ARG A 162 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 100 through 105 removed outlier: 4.743A pdb=" N ALA E 159 " --> pdb=" O GLY E 125 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU E 154 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER E 160 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 150 " --> pdb=" O CYS E 162 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS E 164 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN E 148 " --> pdb=" O LYS E 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AA9, first strand: chain 'E' and resid 208 through 209 removed outlier: 3.756A pdb=" N THR E 225 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP E 230 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR E 264 " --> pdb=" O ASP E 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 238 through 243 Processing sheet with id=AB2, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.257A pdb=" N THR E 329 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N PHE E 371 " --> pdb=" O ASN E 334 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.257A pdb=" N THR E 329 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N PHE E 371 " --> pdb=" O ASN E 334 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 362 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 341 through 344 removed outlier: 3.820A pdb=" N LYS E 407 " --> pdb=" O CYS E 392 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 100 through 105 Processing sheet with id=AB6, first strand: chain 'F' and resid 134 through 136 Processing sheet with id=AB7, first strand: chain 'F' and resid 205 through 209 removed outlier: 3.656A pdb=" N ILE F 205 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP F 230 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR F 264 " --> pdb=" O ASP F 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 238 through 243 Processing sheet with id=AB9, first strand: chain 'F' and resid 311 through 315 removed outlier: 4.287A pdb=" N THR F 329 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 349 through 350 439 hydrogen bonds defined for protein. 1197 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: 2.59 Time building geometry restraints manager: 3.13 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: 1412 1.30 - 1.43: 2385 1.43 - 1.56: 5297 1.56 - 1.69: 2 1.69 - 1.82: 53 Bond restraints: 9149 Sorted by residual: bond pdb=" C PHE A 207 " pdb=" O PHE A 207 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.28e-02 6.10e+03 2.59e+01 bond pdb=" C ILE A 206 " pdb=" O ILE A 206 " ideal model delta sigma weight residual 1.237 1.186 0.052 1.17e-02 7.31e+03 1.95e+01 bond pdb=" C ILE A 213 " pdb=" O ILE A 213 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.13e-02 7.83e+03 1.88e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C VAL A 211 " pdb=" O VAL A 211 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.17e-02 7.31e+03 1.68e+01 ... (remaining 9144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 12279 3.24 - 6.47: 141 6.47 - 9.71: 17 9.71 - 12.94: 3 12.94 - 16.18: 3 Bond angle restraints: 12443 Sorted by residual: angle pdb=" CB GLU B 171 " pdb=" CG GLU B 171 " pdb=" CD GLU B 171 " ideal model delta sigma weight residual 112.60 96.42 16.18 1.70e+00 3.46e-01 9.06e+01 angle pdb=" C ILE A 213 " pdb=" CA ILE A 213 " pdb=" CB ILE A 213 " ideal model delta sigma weight residual 111.97 102.70 9.27 1.28e+00 6.10e-01 5.24e+01 angle pdb=" N LEU A 205 " pdb=" CA LEU A 205 " pdb=" C LEU A 205 " ideal model delta sigma weight residual 113.18 105.05 8.13 1.21e+00 6.83e-01 4.52e+01 angle pdb=" N GLU B 171 " pdb=" CA GLU B 171 " pdb=" C GLU B 171 " ideal model delta sigma weight residual 111.03 103.75 7.28 1.11e+00 8.12e-01 4.30e+01 angle pdb=" C ARG A 179 " pdb=" CA ARG A 179 " pdb=" CB ARG A 179 " ideal model delta sigma weight residual 110.42 123.45 -13.03 1.99e+00 2.53e-01 4.29e+01 ... (remaining 12438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 5298 24.44 - 48.89: 384 48.89 - 73.33: 51 73.33 - 97.78: 34 97.78 - 122.22: 22 Dihedral angle restraints: 5789 sinusoidal: 2598 harmonic: 3191 Sorted by residual: dihedral pdb=" CB CYS G 25 " pdb=" SG CYS G 25 " pdb=" SG CYS H 25 " pdb=" CB CYS H 25 " ideal model delta sinusoidal sigma weight residual -86.00 -175.19 89.19 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" N GLU B 171 " pdb=" C GLU B 171 " pdb=" CA GLU B 171 " pdb=" CB GLU B 171 " ideal model delta harmonic sigma weight residual 122.80 107.21 15.59 0 2.50e+00 1.60e-01 3.89e+01 dihedral pdb=" C GLU B 171 " pdb=" N GLU B 171 " pdb=" CA GLU B 171 " pdb=" CB GLU B 171 " ideal model delta harmonic sigma weight residual -122.60 -107.65 -14.95 0 2.50e+00 1.60e-01 3.58e+01 ... (remaining 5786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1417 0.098 - 0.196: 77 0.196 - 0.293: 10 0.293 - 0.391: 5 0.391 - 0.489: 1 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CA GLU B 171 " pdb=" N GLU B 171 " pdb=" C GLU B 171 " pdb=" CB GLU B 171 " both_signs ideal model delta sigma weight residual False 2.51 3.00 -0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.82 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 238 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 1507 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 204 " 0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C GLN A 204 " -0.084 2.00e-02 2.50e+03 pdb=" O GLN A 204 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU A 205 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 171 " 0.020 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" CD GLU B 171 " -0.073 2.00e-02 2.50e+03 pdb=" OE1 GLU B 171 " 0.027 2.00e-02 2.50e+03 pdb=" OE2 GLU B 171 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 200 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C GLU F 200 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU F 200 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO F 201 " 0.021 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 104 2.60 - 3.18: 7586 3.18 - 3.75: 13419 3.75 - 4.33: 18061 4.33 - 4.90: 29961 Nonbonded interactions: 69131 Sorted by model distance: nonbonded pdb=" O LEU A 203 " pdb=" N ILE A 206 " model vdw 2.026 3.120 nonbonded pdb=" OE1 GLN E 118 " pdb=" NZ LYS E 164 " model vdw 2.198 3.120 nonbonded pdb=" O ASP A 168 " pdb=" OH TYR A 172 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR E 120 " pdb=" OE2 GLU F 102 " model vdw 2.278 3.040 nonbonded pdb=" O TYR B 193 " pdb=" NE2 GLN B 197 " model vdw 2.284 3.120 ... (remaining 69126 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' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 22 through 58) } ncs_group { reference = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.530 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 9184 Z= 0.262 Angle : 0.891 16.180 12536 Z= 0.469 Chirality : 0.053 0.489 1510 Planarity : 0.005 0.070 1519 Dihedral : 18.711 122.219 3683 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.16 % Favored : 93.47 % Rotamer: Outliers : 0.61 % Allowed : 12.59 % Favored : 86.80 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 10.64 % 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: 0.17 (0.26), residues: 1072 helix: 2.02 (0.31), residues: 265 sheet: 0.26 (0.27), residues: 364 loop : -1.19 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 172 HIS 0.008 0.001 HIS E 105 PHE 0.013 0.001 PHE A 207 TYR 0.018 0.001 TYR F 313 ARG 0.008 0.001 ARG E 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00895 ( 11) link_NAG-ASN : angle 4.81424 ( 33) link_ALPHA1-6 : bond 0.00472 ( 2) link_ALPHA1-6 : angle 1.51719 ( 6) link_BETA1-4 : bond 0.00868 ( 8) link_BETA1-4 : angle 1.82939 ( 24) link_ALPHA1-3 : bond 0.00426 ( 2) link_ALPHA1-3 : angle 1.44986 ( 6) hydrogen bonds : bond 0.10335 ( 420) hydrogen bonds : angle 5.01032 ( 1197) SS BOND : bond 0.00355 ( 12) SS BOND : angle 1.07058 ( 24) covalent geometry : bond 0.00473 ( 9149) covalent geometry : angle 0.85287 (12443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 252 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 43 TYR cc_start: 0.8488 (t80) cc_final: 0.8124 (t80) REVERT: H 26 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: H 28 LEU cc_start: 0.8222 (tt) cc_final: 0.7979 (tt) REVERT: B 123 LEU cc_start: 0.8378 (tp) cc_final: 0.7901 (tt) REVERT: E 135 TRP cc_start: 0.8321 (m100) cc_final: 0.7796 (m-10) outliers start: 6 outliers final: 2 residues processed: 257 average time/residue: 0.1998 time to fit residues: 70.7023 Evaluate side-chains 193 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain H residue 26 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN B 126 ASN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.170458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.140450 restraints weight = 15398.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143101 restraints weight = 9401.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.145230 restraints weight = 6633.881| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9184 Z= 0.174 Angle : 0.769 10.456 12536 Z= 0.365 Chirality : 0.047 0.329 1510 Planarity : 0.004 0.055 1519 Dihedral : 14.247 110.799 1631 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.22 % Favored : 94.31 % Rotamer: Outliers : 3.05 % Allowed : 18.27 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1072 helix: 1.68 (0.30), residues: 260 sheet: 0.23 (0.27), residues: 378 loop : -1.18 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 42 HIS 0.003 0.001 HIS E 396 PHE 0.022 0.002 PHE E 335 TYR 0.022 0.002 TYR B 193 ARG 0.006 0.001 ARG G 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 11) link_NAG-ASN : angle 4.67283 ( 33) link_ALPHA1-6 : bond 0.00246 ( 2) link_ALPHA1-6 : angle 2.49235 ( 6) link_BETA1-4 : bond 0.00420 ( 8) link_BETA1-4 : angle 2.70908 ( 24) link_ALPHA1-3 : bond 0.00897 ( 2) link_ALPHA1-3 : angle 2.14691 ( 6) hydrogen bonds : bond 0.03973 ( 420) hydrogen bonds : angle 4.49872 ( 1197) SS BOND : bond 0.00963 ( 12) SS BOND : angle 1.38328 ( 24) covalent geometry : bond 0.00401 ( 9149) covalent geometry : angle 0.71699 (12443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7458 (t) REVERT: H 26 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: B 81 ASP cc_start: 0.8767 (p0) cc_final: 0.8224 (p0) REVERT: B 83 GLU cc_start: 0.7764 (pm20) cc_final: 0.7340 (pm20) REVERT: B 106 LEU cc_start: 0.9145 (mt) cc_final: 0.8906 (tp) REVERT: B 171 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7626 (tt0) outliers start: 30 outliers final: 16 residues processed: 214 average time/residue: 0.2014 time to fit residues: 59.5978 Evaluate side-chains 186 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 258 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 0.0570 chunk 69 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.161308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.131447 restraints weight = 15707.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131634 restraints weight = 10212.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.132968 restraints weight = 9244.707| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9184 Z= 0.232 Angle : 0.800 9.702 12536 Z= 0.389 Chirality : 0.050 0.346 1510 Planarity : 0.005 0.056 1519 Dihedral : 12.686 109.354 1627 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.97 % Favored : 93.66 % Rotamer: Outliers : 4.67 % Allowed : 18.58 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.19 (0.26), residues: 1072 helix: 1.53 (0.29), residues: 266 sheet: -0.02 (0.27), residues: 375 loop : -1.23 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 277 HIS 0.007 0.002 HIS A 65 PHE 0.022 0.002 PHE B 148 TYR 0.042 0.002 TYR G 43 ARG 0.005 0.001 ARG G 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 11) link_NAG-ASN : angle 4.66340 ( 33) link_ALPHA1-6 : bond 0.00139 ( 2) link_ALPHA1-6 : angle 2.86885 ( 6) link_BETA1-4 : bond 0.00401 ( 8) link_BETA1-4 : angle 2.59547 ( 24) link_ALPHA1-3 : bond 0.00662 ( 2) link_ALPHA1-3 : angle 1.29579 ( 6) hydrogen bonds : bond 0.04387 ( 420) hydrogen bonds : angle 4.72142 ( 1197) SS BOND : bond 0.00518 ( 12) SS BOND : angle 1.53030 ( 24) covalent geometry : bond 0.00540 ( 9149) covalent geometry : angle 0.75193 (12443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8567 (tp) cc_final: 0.8244 (tt) REVERT: A 128 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: A 226 GLU cc_start: 0.8292 (pt0) cc_final: 0.7734 (pt0) REVERT: H 26 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.6148 (m-80) REVERT: B 81 ASP cc_start: 0.8910 (p0) cc_final: 0.8686 (p0) REVERT: B 95 TRP cc_start: 0.5533 (t60) cc_final: 0.4004 (t60) REVERT: B 185 CYS cc_start: 0.7567 (t) cc_final: 0.7234 (t) REVERT: E 296 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8158 (pt) REVERT: E 319 GLU cc_start: 0.5621 (tt0) cc_final: 0.5405 (tp30) REVERT: F 255 TYR cc_start: 0.7584 (p90) cc_final: 0.7198 (p90) REVERT: F 362 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6780 (mp) outliers start: 46 outliers final: 20 residues processed: 209 average time/residue: 0.2087 time to fit residues: 60.4660 Evaluate side-chains 187 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 9.9990 chunk 76 optimal weight: 0.0270 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131001 restraints weight = 15365.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.134031 restraints weight = 10448.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135176 restraints weight = 7195.398| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9184 Z= 0.148 Angle : 0.740 9.895 12536 Z= 0.356 Chirality : 0.047 0.353 1510 Planarity : 0.004 0.059 1519 Dihedral : 11.836 107.186 1627 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.41 % Favored : 94.31 % Rotamer: Outliers : 4.26 % Allowed : 21.02 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.14 (0.26), residues: 1072 helix: 1.60 (0.31), residues: 263 sheet: 0.03 (0.28), residues: 374 loop : -1.24 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 42 HIS 0.004 0.001 HIS E 105 PHE 0.016 0.001 PHE E 335 TYR 0.018 0.001 TYR G 43 ARG 0.007 0.001 ARG B 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 11) link_NAG-ASN : angle 4.10922 ( 33) link_ALPHA1-6 : bond 0.00382 ( 2) link_ALPHA1-6 : angle 2.44179 ( 6) link_BETA1-4 : bond 0.00463 ( 8) link_BETA1-4 : angle 2.51106 ( 24) link_ALPHA1-3 : bond 0.01041 ( 2) link_ALPHA1-3 : angle 1.56226 ( 6) hydrogen bonds : bond 0.04067 ( 420) hydrogen bonds : angle 4.59293 ( 1197) SS BOND : bond 0.00425 ( 12) SS BOND : angle 1.24107 ( 24) covalent geometry : bond 0.00336 ( 9149) covalent geometry : angle 0.69848 (12443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8456 (tp) cc_final: 0.8122 (tt) REVERT: A 128 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.7947 (m-30) REVERT: A 226 GLU cc_start: 0.8331 (pt0) cc_final: 0.7738 (pt0) REVERT: H 26 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6258 (m-10) REVERT: B 95 TRP cc_start: 0.5501 (OUTLIER) cc_final: 0.4019 (t60) REVERT: B 120 ARG cc_start: 0.7736 (mtt90) cc_final: 0.7449 (mtt90) REVERT: B 171 GLU cc_start: 0.7630 (tt0) cc_final: 0.7256 (tt0) REVERT: B 185 CYS cc_start: 0.7545 (t) cc_final: 0.7221 (t) REVERT: E 296 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.8045 (pt) REVERT: F 255 TYR cc_start: 0.7564 (p90) cc_final: 0.7218 (p90) outliers start: 42 outliers final: 30 residues processed: 195 average time/residue: 0.2044 time to fit residues: 55.4320 Evaluate side-chains 198 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 80 optimal weight: 0.0980 chunk 102 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.161749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.130901 restraints weight = 15445.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.133006 restraints weight = 10055.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134947 restraints weight = 7407.993| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9184 Z= 0.158 Angle : 0.727 8.210 12536 Z= 0.352 Chirality : 0.047 0.356 1510 Planarity : 0.004 0.060 1519 Dihedral : 11.345 104.390 1627 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.25 % Favored : 93.47 % Rotamer: Outliers : 4.77 % Allowed : 21.12 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.22 (0.27), residues: 1072 helix: 1.44 (0.31), residues: 270 sheet: 0.05 (0.28), residues: 371 loop : -1.33 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 135 HIS 0.004 0.001 HIS E 396 PHE 0.014 0.001 PHE E 335 TYR 0.015 0.001 TYR G 43 ARG 0.006 0.001 ARG B 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 11) link_NAG-ASN : angle 3.95076 ( 33) link_ALPHA1-6 : bond 0.00404 ( 2) link_ALPHA1-6 : angle 2.53618 ( 6) link_BETA1-4 : bond 0.00401 ( 8) link_BETA1-4 : angle 2.45247 ( 24) link_ALPHA1-3 : bond 0.01058 ( 2) link_ALPHA1-3 : angle 1.53139 ( 6) hydrogen bonds : bond 0.03982 ( 420) hydrogen bonds : angle 4.54734 ( 1197) SS BOND : bond 0.00474 ( 12) SS BOND : angle 1.22616 ( 24) covalent geometry : bond 0.00365 ( 9149) covalent geometry : angle 0.68706 (12443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8530 (tp) cc_final: 0.8216 (tt) REVERT: A 128 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: A 226 GLU cc_start: 0.8360 (pt0) cc_final: 0.7753 (pt0) REVERT: H 26 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6111 (m-10) REVERT: B 95 TRP cc_start: 0.5693 (OUTLIER) cc_final: 0.4046 (t60) REVERT: B 171 GLU cc_start: 0.7755 (tt0) cc_final: 0.7442 (tt0) REVERT: B 176 MET cc_start: 0.7840 (mtm) cc_final: 0.7628 (mtm) REVERT: B 185 CYS cc_start: 0.7544 (t) cc_final: 0.7179 (t) REVERT: E 345 LEU cc_start: 0.8168 (mt) cc_final: 0.7937 (tp) REVERT: F 255 TYR cc_start: 0.7663 (p90) cc_final: 0.7327 (p90) REVERT: F 362 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6482 (mp) outliers start: 47 outliers final: 31 residues processed: 210 average time/residue: 0.2210 time to fit residues: 64.8300 Evaluate side-chains 208 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 ASN ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** 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 = 0.4110 r_free = 0.4110 target = 0.161546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130986 restraints weight = 15549.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.133264 restraints weight = 9955.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134893 restraints weight = 7327.492| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9184 Z= 0.156 Angle : 0.754 13.234 12536 Z= 0.359 Chirality : 0.048 0.355 1510 Planarity : 0.004 0.062 1519 Dihedral : 10.992 102.231 1627 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.97 % Favored : 93.75 % Rotamer: Outliers : 4.57 % Allowed : 21.73 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.21 (0.27), residues: 1072 helix: 1.37 (0.31), residues: 269 sheet: 0.04 (0.28), residues: 370 loop : -1.22 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 135 HIS 0.004 0.001 HIS E 396 PHE 0.013 0.001 PHE E 335 TYR 0.026 0.002 TYR G 43 ARG 0.006 0.001 ARG G 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 11) link_NAG-ASN : angle 3.77987 ( 33) link_ALPHA1-6 : bond 0.00464 ( 2) link_ALPHA1-6 : angle 2.57269 ( 6) link_BETA1-4 : bond 0.00421 ( 8) link_BETA1-4 : angle 2.36814 ( 24) link_ALPHA1-3 : bond 0.01061 ( 2) link_ALPHA1-3 : angle 1.47786 ( 6) hydrogen bonds : bond 0.04045 ( 420) hydrogen bonds : angle 4.57991 ( 1197) SS BOND : bond 0.00498 ( 12) SS BOND : angle 1.27652 ( 24) covalent geometry : bond 0.00360 ( 9149) covalent geometry : angle 0.71903 (12443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 179 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8529 (tp) cc_final: 0.8317 (tt) REVERT: A 226 GLU cc_start: 0.8287 (pt0) cc_final: 0.7682 (pt0) REVERT: H 26 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.6218 (m-10) REVERT: H 29 ASP cc_start: 0.8263 (m-30) cc_final: 0.7869 (m-30) REVERT: B 95 TRP cc_start: 0.5657 (OUTLIER) cc_final: 0.3983 (t60) REVERT: B 171 GLU cc_start: 0.7765 (tt0) cc_final: 0.7461 (tt0) REVERT: B 185 CYS cc_start: 0.7461 (t) cc_final: 0.7119 (t) REVERT: E 137 MET cc_start: 0.6611 (ttt) cc_final: 0.6194 (ttt) REVERT: E 319 GLU cc_start: 0.6021 (tp30) cc_final: 0.5670 (tp30) REVERT: E 345 LEU cc_start: 0.8148 (mt) cc_final: 0.7856 (tp) REVERT: F 222 PRO cc_start: 0.8815 (Cg_exo) cc_final: 0.8512 (Cg_endo) REVERT: F 255 TYR cc_start: 0.7648 (p90) cc_final: 0.7381 (p90) REVERT: F 269 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8521 (mt) REVERT: F 362 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6489 (mp) outliers start: 45 outliers final: 37 residues processed: 206 average time/residue: 0.2108 time to fit residues: 60.3058 Evaluate side-chains 207 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN B 153 ASN E 114 HIS ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.155692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.124829 restraints weight = 15637.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125317 restraints weight = 9916.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125931 restraints weight = 8750.138| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 9184 Z= 0.256 Angle : 0.837 11.543 12536 Z= 0.405 Chirality : 0.050 0.344 1510 Planarity : 0.005 0.063 1519 Dihedral : 11.589 100.194 1627 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.46 % Favored : 92.26 % Rotamer: Outliers : 5.58 % Allowed : 22.03 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1072 helix: 1.18 (0.30), residues: 272 sheet: -0.24 (0.28), residues: 370 loop : -1.28 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 135 HIS 0.006 0.002 HIS F 396 PHE 0.015 0.002 PHE A 151 TYR 0.026 0.002 TYR G 43 ARG 0.007 0.001 ARG G 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 11) link_NAG-ASN : angle 4.27279 ( 33) link_ALPHA1-6 : bond 0.00114 ( 2) link_ALPHA1-6 : angle 3.00004 ( 6) link_BETA1-4 : bond 0.00513 ( 8) link_BETA1-4 : angle 2.56448 ( 24) link_ALPHA1-3 : bond 0.00853 ( 2) link_ALPHA1-3 : angle 1.54313 ( 6) hydrogen bonds : bond 0.04473 ( 420) hydrogen bonds : angle 4.84863 ( 1197) SS BOND : bond 0.00540 ( 12) SS BOND : angle 1.53367 ( 24) covalent geometry : bond 0.00610 ( 9149) covalent geometry : angle 0.79707 (12443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.8210 (pt0) cc_final: 0.7755 (pt0) REVERT: H 26 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.6443 (m-10) REVERT: B 83 GLU cc_start: 0.7929 (pm20) cc_final: 0.7483 (pm20) REVERT: B 95 TRP cc_start: 0.6263 (OUTLIER) cc_final: 0.4958 (t60) REVERT: B 171 GLU cc_start: 0.7767 (tt0) cc_final: 0.7411 (tt0) REVERT: B 185 CYS cc_start: 0.7534 (t) cc_final: 0.7188 (t) REVERT: E 137 MET cc_start: 0.6504 (ttt) cc_final: 0.6242 (ttt) REVERT: E 319 GLU cc_start: 0.6213 (tp30) cc_final: 0.5761 (tp30) REVERT: F 137 MET cc_start: 0.7491 (ttt) cc_final: 0.7144 (ttt) REVERT: F 255 TYR cc_start: 0.7781 (p90) cc_final: 0.7453 (p90) REVERT: F 362 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6797 (mp) outliers start: 55 outliers final: 41 residues processed: 204 average time/residue: 0.2013 time to fit residues: 57.1108 Evaluate side-chains 203 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.158666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128060 restraints weight = 15770.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.128482 restraints weight = 9853.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.129310 restraints weight = 8694.286| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9184 Z= 0.157 Angle : 0.770 14.119 12536 Z= 0.367 Chirality : 0.048 0.345 1510 Planarity : 0.004 0.062 1519 Dihedral : 10.973 98.730 1627 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.44 % Favored : 93.28 % Rotamer: Outliers : 4.87 % Allowed : 22.94 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.37 (0.27), residues: 1072 helix: 1.24 (0.31), residues: 272 sheet: -0.14 (0.28), residues: 368 loop : -1.25 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 135 HIS 0.004 0.001 HIS E 396 PHE 0.015 0.001 PHE H 33 TYR 0.019 0.001 TYR G 43 ARG 0.014 0.001 ARG E 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 11) link_NAG-ASN : angle 3.84678 ( 33) link_ALPHA1-6 : bond 0.00475 ( 2) link_ALPHA1-6 : angle 2.64346 ( 6) link_BETA1-4 : bond 0.00440 ( 8) link_BETA1-4 : angle 2.24997 ( 24) link_ALPHA1-3 : bond 0.01050 ( 2) link_ALPHA1-3 : angle 1.35485 ( 6) hydrogen bonds : bond 0.04208 ( 420) hydrogen bonds : angle 4.70489 ( 1197) SS BOND : bond 0.00530 ( 12) SS BOND : angle 1.34880 ( 24) covalent geometry : bond 0.00363 ( 9149) covalent geometry : angle 0.73472 (12443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6443 (tpp) cc_final: 0.6123 (tpt) REVERT: A 114 LEU cc_start: 0.8590 (tp) cc_final: 0.8271 (tt) REVERT: A 226 GLU cc_start: 0.8196 (pt0) cc_final: 0.7748 (pt0) REVERT: G 52 LYS cc_start: 0.8401 (ttpp) cc_final: 0.8074 (pttm) REVERT: H 26 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.6176 (m-10) REVERT: B 83 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: B 95 TRP cc_start: 0.6040 (OUTLIER) cc_final: 0.4432 (t60) REVERT: B 151 MET cc_start: 0.7859 (mmm) cc_final: 0.7604 (mmm) REVERT: B 171 GLU cc_start: 0.7870 (tt0) cc_final: 0.7569 (tt0) REVERT: B 185 CYS cc_start: 0.7642 (t) cc_final: 0.7392 (t) REVERT: E 137 MET cc_start: 0.6329 (ttt) cc_final: 0.6121 (ttt) REVERT: E 319 GLU cc_start: 0.6102 (tp30) cc_final: 0.5701 (tp30) REVERT: E 345 LEU cc_start: 0.8228 (mt) cc_final: 0.7991 (tp) REVERT: F 255 TYR cc_start: 0.7696 (p90) cc_final: 0.7369 (p90) REVERT: F 362 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6592 (mp) outliers start: 48 outliers final: 34 residues processed: 196 average time/residue: 0.1933 time to fit residues: 53.4363 Evaluate side-chains 198 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 HIS ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.158913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128326 restraints weight = 15558.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.130122 restraints weight = 9757.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.131578 restraints weight = 7863.211| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9184 Z= 0.150 Angle : 0.768 13.785 12536 Z= 0.365 Chirality : 0.048 0.344 1510 Planarity : 0.004 0.065 1519 Dihedral : 10.612 96.054 1627 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.53 % Favored : 93.19 % Rotamer: Outliers : 4.06 % Allowed : 23.25 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.35 (0.27), residues: 1072 helix: 1.22 (0.31), residues: 272 sheet: -0.10 (0.28), residues: 367 loop : -1.23 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 135 HIS 0.004 0.001 HIS E 105 PHE 0.014 0.001 PHE F 113 TYR 0.020 0.001 TYR G 43 ARG 0.011 0.001 ARG E 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 11) link_NAG-ASN : angle 3.76057 ( 33) link_ALPHA1-6 : bond 0.00557 ( 2) link_ALPHA1-6 : angle 2.54974 ( 6) link_BETA1-4 : bond 0.00471 ( 8) link_BETA1-4 : angle 2.21902 ( 24) link_ALPHA1-3 : bond 0.01006 ( 2) link_ALPHA1-3 : angle 1.41703 ( 6) hydrogen bonds : bond 0.04133 ( 420) hydrogen bonds : angle 4.68566 ( 1197) SS BOND : bond 0.00537 ( 12) SS BOND : angle 1.11721 ( 24) covalent geometry : bond 0.00348 ( 9149) covalent geometry : angle 0.73562 (12443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6391 (tpp) cc_final: 0.6112 (tpt) REVERT: A 114 LEU cc_start: 0.8575 (tp) cc_final: 0.8257 (tt) REVERT: A 226 GLU cc_start: 0.8255 (pt0) cc_final: 0.7852 (pt0) REVERT: G 45 ARG cc_start: 0.8363 (ttt180) cc_final: 0.7784 (ttm170) REVERT: H 26 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6091 (m-10) REVERT: B 83 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: B 95 TRP cc_start: 0.6126 (OUTLIER) cc_final: 0.4500 (t60) REVERT: B 151 MET cc_start: 0.7850 (mmm) cc_final: 0.7610 (mmm) REVERT: B 171 GLU cc_start: 0.7834 (tt0) cc_final: 0.7631 (tt0) REVERT: B 185 CYS cc_start: 0.7678 (t) cc_final: 0.7430 (t) REVERT: E 319 GLU cc_start: 0.6118 (tp30) cc_final: 0.5737 (tp30) REVERT: E 345 LEU cc_start: 0.8221 (mt) cc_final: 0.7910 (tp) REVERT: F 255 TYR cc_start: 0.7799 (p90) cc_final: 0.7468 (p90) REVERT: F 362 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6585 (mp) outliers start: 40 outliers final: 34 residues processed: 190 average time/residue: 0.2125 time to fit residues: 55.7147 Evaluate side-chains 197 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 0.0010 chunk 65 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.159638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129113 restraints weight = 15652.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129465 restraints weight = 9895.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.131488 restraints weight = 8293.732| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9184 Z= 0.149 Angle : 0.783 14.214 12536 Z= 0.370 Chirality : 0.048 0.340 1510 Planarity : 0.004 0.064 1519 Dihedral : 10.351 93.322 1627 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.62 % Favored : 93.10 % Rotamer: Outliers : 4.06 % Allowed : 23.86 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.33 (0.27), residues: 1072 helix: 1.23 (0.31), residues: 269 sheet: -0.09 (0.28), residues: 367 loop : -1.20 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 135 HIS 0.004 0.001 HIS E 105 PHE 0.015 0.001 PHE H 33 TYR 0.021 0.001 TYR G 43 ARG 0.010 0.001 ARG E 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 11) link_NAG-ASN : angle 3.64439 ( 33) link_ALPHA1-6 : bond 0.00611 ( 2) link_ALPHA1-6 : angle 2.51100 ( 6) link_BETA1-4 : bond 0.00488 ( 8) link_BETA1-4 : angle 2.15742 ( 24) link_ALPHA1-3 : bond 0.01038 ( 2) link_ALPHA1-3 : angle 1.40837 ( 6) hydrogen bonds : bond 0.04089 ( 420) hydrogen bonds : angle 4.66193 ( 1197) SS BOND : bond 0.00540 ( 12) SS BOND : angle 1.16815 ( 24) covalent geometry : bond 0.00345 ( 9149) covalent geometry : angle 0.75301 (12443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8555 (tp) cc_final: 0.8244 (tt) REVERT: A 226 GLU cc_start: 0.8180 (pt0) cc_final: 0.7915 (pt0) REVERT: G 45 ARG cc_start: 0.8302 (ttt180) cc_final: 0.7804 (ttm170) REVERT: H 26 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6104 (m-10) REVERT: H 29 ASP cc_start: 0.8459 (m-30) cc_final: 0.8102 (m-30) REVERT: B 95 TRP cc_start: 0.6051 (OUTLIER) cc_final: 0.4407 (t60) REVERT: B 151 MET cc_start: 0.7864 (mmm) cc_final: 0.7577 (mmm) REVERT: B 168 PHE cc_start: 0.8539 (t80) cc_final: 0.8310 (t80) REVERT: B 185 CYS cc_start: 0.7724 (t) cc_final: 0.7422 (t) REVERT: F 255 TYR cc_start: 0.7760 (p90) cc_final: 0.7432 (p90) REVERT: F 362 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6573 (mp) outliers start: 40 outliers final: 35 residues processed: 190 average time/residue: 0.2028 time to fit residues: 54.4038 Evaluate side-chains 198 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 26 TYR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 241 TRP Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 392 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 0.0060 chunk 103 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.159488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.128927 restraints weight = 15710.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129283 restraints weight = 9930.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130795 restraints weight = 8544.404| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9184 Z= 0.150 Angle : 0.801 14.504 12536 Z= 0.375 Chirality : 0.048 0.329 1510 Planarity : 0.004 0.065 1519 Dihedral : 10.152 89.824 1627 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.72 % Favored : 93.00 % Rotamer: Outliers : 3.65 % Allowed : 24.37 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -0.29 (0.27), residues: 1072 helix: 1.28 (0.31), residues: 269 sheet: -0.05 (0.28), residues: 364 loop : -1.19 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 135 HIS 0.004 0.001 HIS E 396 PHE 0.020 0.002 PHE E 178 TYR 0.021 0.001 TYR G 43 ARG 0.009 0.001 ARG E 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 11) link_NAG-ASN : angle 3.61002 ( 33) link_ALPHA1-6 : bond 0.00583 ( 2) link_ALPHA1-6 : angle 2.45252 ( 6) link_BETA1-4 : bond 0.00482 ( 8) link_BETA1-4 : angle 2.11924 ( 24) link_ALPHA1-3 : bond 0.01037 ( 2) link_ALPHA1-3 : angle 1.43113 ( 6) hydrogen bonds : bond 0.04099 ( 420) hydrogen bonds : angle 4.66036 ( 1197) SS BOND : bond 0.00515 ( 12) SS BOND : angle 1.09851 ( 24) covalent geometry : bond 0.00349 ( 9149) covalent geometry : angle 0.77267 (12443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3003.85 seconds wall clock time: 53 minutes 3.54 seconds (3183.54 seconds total)