Starting phenix.real_space_refine on Mon Jul 22 00:17:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/07_2024/7ooa_13008.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/07_2024/7ooa_13008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/07_2024/7ooa_13008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/07_2024/7ooa_13008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/07_2024/7ooa_13008.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ooa_13008/07_2024/7ooa_13008.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 42 5.16 5 C 10171 2.51 5 N 2450 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15610 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "B" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "C" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "D" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "F" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "G" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "A" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 25 Chain: "B" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 25 Chain: "C" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 25 Chain: "D" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 25 Chain: "E" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 25 Chain: "F" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 25 Chain: "G" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 234 Unusual residues: {'AV0': 3, 'LMT': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 25 Time building chain proxies: 8.56, per 1000 atoms: 0.55 Number of scatterers: 15610 At special positions: 0 Unit cell: (98.9055, 98.9055, 138.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 7 15.00 O 2940 8.00 N 2450 7.00 C 10171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.99 Conformation dependent library (CDL) restraints added in 2.5 seconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 56.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 20 through 59 removed outlier: 4.186A pdb=" N LEU A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 Processing helix chain 'A' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 20 through 59 removed outlier: 4.185A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 89 Processing helix chain 'B' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 20 through 59 removed outlier: 4.186A pdb=" N LEU C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 89 Processing helix chain 'C' and resid 92 through 128 removed outlier: 5.366A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 20 through 59 removed outlier: 4.186A pdb=" N LEU D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 89 Processing helix chain 'D' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 20 through 59 removed outlier: 4.186A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 89 Processing helix chain 'E' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 20 through 59 removed outlier: 4.186A pdb=" N LEU F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 89 Processing helix chain 'F' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 removed outlier: 3.570A pdb=" N GLY F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 245 through 265 Processing helix chain 'G' and resid 20 through 59 removed outlier: 4.185A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 89 Processing helix chain 'G' and resid 92 through 128 removed outlier: 5.365A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 173 removed outlier: 3.571A pdb=" N GLY G 173 " --> pdb=" O LYS G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.713A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.617A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 279 removed outlier: 8.212A pdb=" N MET E 273 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP D 274 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS D 278 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ARG E 279 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N MET G 273 " --> pdb=" O GLN F 272 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP F 274 " --> pdb=" O MET G 273 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL G 275 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N PHE G 277 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS F 278 " --> pdb=" O PHE G 277 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ARG G 279 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET A 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LYS G 278 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 275 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.617A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.618A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.617A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.617A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.617A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.618A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 3168 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: 4.70 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2311 1.32 - 1.44: 3961 1.44 - 1.56: 9443 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 15813 Sorted by residual: bond pdb=" C4 PEE G 303 " pdb=" O4P PEE G 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C4 PEE B 303 " pdb=" O4P PEE B 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C4 PEE E 303 " pdb=" O4P PEE E 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C4 PEE C 303 " pdb=" O4P PEE C 303 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.21e+00 ... (remaining 15808 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.25: 333 107.25 - 113.94: 9999 113.94 - 120.63: 6010 120.63 - 127.32: 4896 127.32 - 134.01: 63 Bond angle restraints: 21301 Sorted by residual: angle pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 92.91 105.04 -12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O3P PEE D 303 " pdb=" P PEE D 303 " pdb=" O4P PEE D 303 " ideal model delta sigma weight residual 92.91 105.04 -12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O3P PEE G 303 " pdb=" P PEE G 303 " pdb=" O4P PEE G 303 " ideal model delta sigma weight residual 92.91 105.04 -12.13 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O3P PEE C 303 " pdb=" P PEE C 303 " pdb=" O4P PEE C 303 " ideal model delta sigma weight residual 92.91 105.03 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O3P PEE E 303 " pdb=" P PEE E 303 " pdb=" O4P PEE E 303 " ideal model delta sigma weight residual 92.91 105.03 -12.12 3.00e+00 1.11e-01 1.63e+01 ... (remaining 21296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.55: 10339 25.55 - 51.11: 301 51.11 - 76.66: 112 76.66 - 102.22: 84 102.22 - 127.77: 140 Dihedral angle restraints: 10976 sinusoidal: 5719 harmonic: 5257 Sorted by residual: dihedral pdb=" C12 PEE E 303 " pdb=" C10 PEE E 303 " pdb=" C11 PEE E 303 " pdb=" O4 PEE E 303 " ideal model delta sinusoidal sigma weight residual -19.47 -147.24 127.77 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C12 PEE A 301 " pdb=" C10 PEE A 301 " pdb=" C11 PEE A 301 " pdb=" O4 PEE A 301 " ideal model delta sinusoidal sigma weight residual -19.47 -147.21 127.74 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C12 PEE D 303 " pdb=" C10 PEE D 303 " pdb=" C11 PEE D 303 " pdb=" O4 PEE D 303 " ideal model delta sinusoidal sigma weight residual -19.47 -147.21 127.74 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 10973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2074 0.050 - 0.100: 474 0.100 - 0.150: 98 0.150 - 0.199: 18 0.199 - 0.249: 17 Chirality restraints: 2681 Sorted by residual: chirality pdb=" C2 PEE C 303 " pdb=" C1 PEE C 303 " pdb=" C3 PEE C 303 " pdb=" O2 PEE C 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C2 PEE A 301 " pdb=" C1 PEE A 301 " pdb=" C3 PEE A 301 " pdb=" O2 PEE A 301 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C2 PEE D 303 " pdb=" C1 PEE D 303 " pdb=" C3 PEE D 303 " pdb=" O2 PEE D 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2678 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 270 " 0.012 5.00e-02 4.00e+02 1.87e-02 5.60e-01 pdb=" N PRO D 271 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO D 271 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO D 271 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 270 " 0.012 5.00e-02 4.00e+02 1.87e-02 5.58e-01 pdb=" N PRO E 271 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO E 271 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO E 271 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 270 " 0.012 5.00e-02 4.00e+02 1.85e-02 5.50e-01 pdb=" N PRO F 271 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO F 271 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO F 271 " 0.010 5.00e-02 4.00e+02 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2897 2.78 - 3.31: 14785 3.31 - 3.84: 25988 3.84 - 4.37: 30771 4.37 - 4.90: 54493 Nonbonded interactions: 128934 Sorted by model distance: nonbonded pdb=" OD2 ASP B 159 " pdb=" NZ LYS B 161 " model vdw 2.256 2.520 nonbonded pdb=" OD2 ASP E 159 " pdb=" NZ LYS E 161 " model vdw 2.256 2.520 nonbonded pdb=" OD2 ASP D 159 " pdb=" NZ LYS D 161 " model vdw 2.256 2.520 nonbonded pdb=" OD2 ASP G 159 " pdb=" NZ LYS G 161 " model vdw 2.256 2.520 nonbonded pdb=" OD2 ASP A 159 " pdb=" NZ LYS A 161 " model vdw 2.256 2.520 ... (remaining 128929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 280 or resid 302 or (resid 305 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 or name CAA or name CAB or n \ ame CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBP or name CBQ or name CBR or name CBS or n \ ame CBT or name CCF or name CCH or name CCJ or name CCL or name CCM or name CCQ \ or name O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name OAL or \ name OAN or name OAP or name OBV or name OBX or name OCB)))) selection = (chain 'B' and (resid 19 through 280 or (resid 302 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 305)) selection = (chain 'C' and (resid 19 through 280 or (resid 302 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 305)) selection = (chain 'D' and (resid 19 through 280 or (resid 302 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 305)) selection = (chain 'E' and (resid 19 through 280 or (resid 302 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 305)) selection = (chain 'F' and (resid 19 through 280 or (resid 302 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 305)) selection = (chain 'G' and (resid 19 through 280 or (resid 302 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 305)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.920 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.070 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 0.041 15813 Z= 0.324 Angle : 0.662 12.132 21301 Z= 0.289 Chirality : 0.047 0.249 2681 Planarity : 0.003 0.019 2450 Dihedral : 21.922 127.771 7588 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.18), residues: 1820 helix: 3.13 (0.15), residues: 1029 sheet: 0.82 (0.29), residues: 280 loop : -0.53 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 251 PHE 0.012 0.002 PHE G 178 TYR 0.006 0.001 TYR E 75 ARG 0.003 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.720 Fit side-chains REVERT: A 105 LEU cc_start: 0.8773 (tp) cc_final: 0.8553 (tp) REVERT: B 92 GLN cc_start: 0.8454 (mt0) cc_final: 0.8233 (mt0) REVERT: C 54 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6997 (mtm-85) REVERT: C 149 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8162 (mm110) REVERT: D 75 TYR cc_start: 0.8614 (m-10) cc_final: 0.8359 (m-80) REVERT: E 75 TYR cc_start: 0.8712 (m-10) cc_final: 0.8464 (m-80) REVERT: G 92 GLN cc_start: 0.8355 (mt0) cc_final: 0.8085 (mt0) outliers start: 0 outliers final: 2 residues processed: 274 average time/residue: 1.7714 time to fit residues: 520.8344 Evaluate side-chains 210 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain G residue 44 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 165 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 149 GLN B 276 ASN C 276 ASN D 92 GLN D 112 GLN F 92 GLN F 112 GLN F 149 GLN F 210 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15813 Z= 0.212 Angle : 0.590 8.180 21301 Z= 0.274 Chirality : 0.041 0.145 2681 Planarity : 0.003 0.033 2450 Dihedral : 17.668 127.072 4463 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.43 % Allowed : 10.11 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.18), residues: 1820 helix: 3.09 (0.15), residues: 1029 sheet: 0.06 (0.33), residues: 175 loop : -0.39 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 240 PHE 0.016 0.002 PHE B 178 TYR 0.009 0.001 TYR B 75 ARG 0.005 0.001 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 241 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8805 (tp) cc_final: 0.8602 (tp) REVERT: C 105 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8276 (tt) REVERT: C 203 GLN cc_start: 0.8158 (pp30) cc_final: 0.7951 (pp30) REVERT: C 210 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: D 126 MET cc_start: 0.8904 (ttp) cc_final: 0.8528 (ttp) REVERT: E 210 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: G 92 GLN cc_start: 0.8323 (mt0) cc_final: 0.8028 (mt0) REVERT: G 210 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7625 (mp10) outliers start: 36 outliers final: 8 residues processed: 256 average time/residue: 1.7361 time to fit residues: 477.1683 Evaluate side-chains 220 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 208 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 149 GLN B 149 GLN D 92 GLN F 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15813 Z= 0.160 Angle : 0.455 4.530 21301 Z= 0.234 Chirality : 0.040 0.125 2681 Planarity : 0.003 0.024 2450 Dihedral : 15.394 122.555 4463 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.29 % Allowed : 11.52 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.18), residues: 1820 helix: 3.22 (0.15), residues: 1029 sheet: 0.14 (0.35), residues: 175 loop : -0.42 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 251 PHE 0.014 0.002 PHE C 277 TYR 0.008 0.001 TYR E 75 ARG 0.006 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 230 time to evaluate : 1.453 Fit side-chains REVERT: A 105 LEU cc_start: 0.8828 (tp) cc_final: 0.8599 (tp) REVERT: A 112 GLN cc_start: 0.7620 (tt0) cc_final: 0.7411 (tt0) REVERT: A 210 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: B 50 ASN cc_start: 0.8792 (m-40) cc_final: 0.8590 (m-40) REVERT: C 105 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8298 (tt) REVERT: C 273 MET cc_start: 0.8473 (tpp) cc_final: 0.7918 (tpp) REVERT: D 54 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6847 (mtp180) REVERT: D 126 MET cc_start: 0.8904 (ttp) cc_final: 0.8564 (ttp) REVERT: D 155 MET cc_start: 0.9190 (ptp) cc_final: 0.8949 (ptm) REVERT: D 210 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: E 210 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: E 278 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6779 (mtmt) REVERT: F 155 MET cc_start: 0.9162 (ptp) cc_final: 0.8915 (ptm) REVERT: G 92 GLN cc_start: 0.8291 (mt0) cc_final: 0.7991 (mt0) REVERT: G 210 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7561 (mp10) outliers start: 34 outliers final: 7 residues processed: 246 average time/residue: 1.7296 time to fit residues: 456.6402 Evaluate side-chains 220 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 207 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN D 92 GLN F 112 GLN F 149 GLN G 30 ASN G 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15813 Z= 0.223 Angle : 0.480 4.530 21301 Z= 0.249 Chirality : 0.040 0.134 2681 Planarity : 0.003 0.029 2450 Dihedral : 15.104 123.359 4459 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.90 % Allowed : 11.93 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.18), residues: 1820 helix: 3.10 (0.15), residues: 1029 sheet: 0.07 (0.33), residues: 175 loop : -0.43 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 251 PHE 0.013 0.002 PHE G 178 TYR 0.011 0.001 TYR B 75 ARG 0.006 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 217 time to evaluate : 1.684 Fit side-chains REVERT: A 105 LEU cc_start: 0.8802 (tp) cc_final: 0.8582 (tp) REVERT: A 112 GLN cc_start: 0.7783 (tt0) cc_final: 0.7572 (tt0) REVERT: A 210 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: B 20 ASN cc_start: 0.2690 (OUTLIER) cc_final: 0.2361 (p0) REVERT: B 210 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.7588 (mp10) REVERT: C 273 MET cc_start: 0.8389 (tpp) cc_final: 0.7865 (tpp) REVERT: D 54 ARG cc_start: 0.7283 (mtp180) cc_final: 0.6890 (mtp180) REVERT: D 155 MET cc_start: 0.9198 (ptp) cc_final: 0.8953 (ptm) REVERT: E 210 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: E 278 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6720 (mtmt) REVERT: F 20 ASN cc_start: 0.2161 (OUTLIER) cc_final: 0.1719 (p0) REVERT: F 155 MET cc_start: 0.9161 (ptp) cc_final: 0.8915 (ptm) REVERT: G 47 MET cc_start: 0.8079 (mtm) cc_final: 0.7817 (mtm) REVERT: G 210 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7515 (mp10) REVERT: G 278 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7089 (mtmt) outliers start: 43 outliers final: 13 residues processed: 241 average time/residue: 1.8019 time to fit residues: 466.0988 Evaluate side-chains 228 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 278 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN D 92 GLN F 30 ASN F 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15813 Z= 0.208 Angle : 0.463 4.571 21301 Z= 0.244 Chirality : 0.040 0.146 2681 Planarity : 0.003 0.030 2450 Dihedral : 14.867 121.681 4459 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 3.03 % Allowed : 12.80 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.18), residues: 1820 helix: 3.11 (0.15), residues: 1029 sheet: 0.09 (0.34), residues: 175 loop : -0.47 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 240 PHE 0.015 0.002 PHE G 277 TYR 0.011 0.001 TYR B 75 ARG 0.009 0.000 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 226 time to evaluate : 1.639 Fit side-chains REVERT: A 105 LEU cc_start: 0.8803 (tp) cc_final: 0.8588 (tp) REVERT: A 112 GLN cc_start: 0.7675 (tt0) cc_final: 0.7446 (tt0) REVERT: A 210 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: B 20 ASN cc_start: 0.2285 (OUTLIER) cc_final: 0.2033 (p0) REVERT: B 210 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: C 20 ASN cc_start: 0.1807 (OUTLIER) cc_final: 0.1457 (p0) REVERT: C 61 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8389 (mt) REVERT: C 210 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.7691 (mp10) REVERT: C 220 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: C 273 MET cc_start: 0.8373 (tpp) cc_final: 0.7818 (tpp) REVERT: D 54 ARG cc_start: 0.7233 (mtp180) cc_final: 0.6834 (mtp180) REVERT: D 210 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: E 210 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: E 278 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6770 (mtmt) REVERT: F 61 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8450 (mt) REVERT: F 155 MET cc_start: 0.9135 (ptp) cc_final: 0.8882 (ptm) REVERT: G 47 MET cc_start: 0.8058 (mtm) cc_final: 0.7797 (mtm) REVERT: G 210 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7529 (mp10) outliers start: 45 outliers final: 13 residues processed: 249 average time/residue: 1.7284 time to fit residues: 462.3218 Evaluate side-chains 235 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 210 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 0.0040 chunk 176 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN D 92 GLN F 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15813 Z= 0.131 Angle : 0.415 4.546 21301 Z= 0.222 Chirality : 0.039 0.124 2681 Planarity : 0.003 0.033 2450 Dihedral : 14.381 121.306 4459 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.02 % Allowed : 13.54 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.18), residues: 1820 helix: 3.30 (0.15), residues: 1029 sheet: 0.88 (0.28), residues: 245 loop : -0.86 (0.21), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 251 PHE 0.015 0.001 PHE E 277 TYR 0.008 0.001 TYR E 75 ARG 0.010 0.000 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 1.684 Fit side-chains REVERT: A 105 LEU cc_start: 0.8808 (tp) cc_final: 0.8587 (tp) REVERT: A 112 GLN cc_start: 0.7601 (tt0) cc_final: 0.7372 (tt0) REVERT: B 210 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: C 20 ASN cc_start: 0.1957 (OUTLIER) cc_final: 0.1656 (p0) REVERT: C 105 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8345 (tt) REVERT: C 273 MET cc_start: 0.8343 (tpp) cc_final: 0.7846 (tpp) REVERT: D 54 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6823 (mtp180) REVERT: D 155 MET cc_start: 0.9205 (ptp) cc_final: 0.8954 (ptm) REVERT: D 210 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: E 210 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: F 20 ASN cc_start: 0.2006 (OUTLIER) cc_final: 0.0723 (p0) REVERT: F 155 MET cc_start: 0.9126 (ptp) cc_final: 0.8876 (ptm) REVERT: G 210 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: G 278 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7188 (mtmt) outliers start: 30 outliers final: 7 residues processed: 237 average time/residue: 1.8060 time to fit residues: 459.2213 Evaluate side-chains 223 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 208 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 278 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN C 112 GLN D 30 ASN D 92 GLN F 112 GLN F 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15813 Z= 0.164 Angle : 0.438 4.466 21301 Z= 0.232 Chirality : 0.039 0.129 2681 Planarity : 0.003 0.034 2450 Dihedral : 14.289 121.528 4459 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.16 % Allowed : 13.27 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.18), residues: 1820 helix: 3.26 (0.15), residues: 1029 sheet: 0.23 (0.27), residues: 280 loop : -0.65 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 240 PHE 0.013 0.002 PHE G 277 TYR 0.008 0.001 TYR D 75 ARG 0.009 0.000 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 1.535 Fit side-chains REVERT: A 105 LEU cc_start: 0.8813 (tp) cc_final: 0.8595 (tp) REVERT: A 112 GLN cc_start: 0.7606 (tt0) cc_final: 0.7362 (tt0) REVERT: A 210 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: B 20 ASN cc_start: 0.1877 (OUTLIER) cc_final: 0.1674 (p0) REVERT: B 210 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: C 20 ASN cc_start: 0.1828 (OUTLIER) cc_final: 0.1539 (p0) REVERT: C 112 GLN cc_start: 0.7651 (tt0) cc_final: 0.7271 (tp40) REVERT: C 273 MET cc_start: 0.8328 (tpp) cc_final: 0.7808 (tpp) REVERT: D 54 ARG cc_start: 0.7176 (mtp180) cc_final: 0.6786 (mtp180) REVERT: D 210 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: E 20 ASN cc_start: 0.2580 (OUTLIER) cc_final: 0.1384 (p0) REVERT: E 210 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: F 20 ASN cc_start: 0.1922 (OUTLIER) cc_final: 0.0634 (p0) REVERT: G 210 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: G 278 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7017 (mtmt) outliers start: 32 outliers final: 9 residues processed: 237 average time/residue: 1.8408 time to fit residues: 467.7485 Evaluate side-chains 224 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 205 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 278 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 119 optimal weight: 0.2980 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN F 112 GLN F 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15813 Z= 0.155 Angle : 0.430 4.520 21301 Z= 0.229 Chirality : 0.039 0.128 2681 Planarity : 0.003 0.035 2450 Dihedral : 14.106 122.270 4459 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.22 % Allowed : 13.48 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.18), residues: 1820 helix: 3.27 (0.15), residues: 1029 sheet: 0.20 (0.27), residues: 280 loop : -0.69 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 240 PHE 0.012 0.001 PHE B 178 TYR 0.007 0.001 TYR D 75 ARG 0.009 0.000 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 1.716 Fit side-chains REVERT: A 105 LEU cc_start: 0.8813 (tp) cc_final: 0.8593 (tp) REVERT: A 112 GLN cc_start: 0.7572 (tt0) cc_final: 0.7328 (tt0) REVERT: B 210 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: B 278 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7121 (mtmt) REVERT: C 20 ASN cc_start: 0.2090 (OUTLIER) cc_final: 0.1836 (p0) REVERT: C 112 GLN cc_start: 0.7661 (tt0) cc_final: 0.7279 (tp40) REVERT: C 273 MET cc_start: 0.8312 (tpp) cc_final: 0.7776 (tpp) REVERT: D 54 ARG cc_start: 0.7172 (mtp180) cc_final: 0.6785 (mtp180) REVERT: D 61 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8475 (mm) REVERT: E 20 ASN cc_start: 0.2592 (OUTLIER) cc_final: 0.1397 (p0) REVERT: E 35 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8349 (mm) REVERT: E 210 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: F 20 ASN cc_start: 0.1859 (OUTLIER) cc_final: 0.0560 (p0) REVERT: G 20 ASN cc_start: 0.2787 (OUTLIER) cc_final: 0.2306 (p0) REVERT: G 210 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: G 278 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7014 (mtmt) outliers start: 33 outliers final: 10 residues processed: 234 average time/residue: 1.7865 time to fit residues: 448.1796 Evaluate side-chains 225 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 278 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 147 optimal weight: 0.0470 chunk 154 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN D 210 GLN F 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15813 Z= 0.132 Angle : 0.419 4.496 21301 Z= 0.224 Chirality : 0.039 0.145 2681 Planarity : 0.003 0.039 2450 Dihedral : 13.796 122.776 4459 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 2.02 % Allowed : 13.88 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.18), residues: 1820 helix: 3.32 (0.15), residues: 1029 sheet: 0.88 (0.27), residues: 245 loop : -0.93 (0.21), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 251 PHE 0.012 0.001 PHE G 178 TYR 0.006 0.001 TYR B 75 ARG 0.010 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 1.648 Fit side-chains REVERT: A 105 LEU cc_start: 0.8791 (tp) cc_final: 0.8573 (tp) REVERT: A 112 GLN cc_start: 0.7565 (tt0) cc_final: 0.7316 (tt0) REVERT: A 210 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: B 210 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7517 (mp10) REVERT: C 20 ASN cc_start: 0.2109 (OUTLIER) cc_final: 0.1896 (p0) REVERT: C 61 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8367 (mt) REVERT: C 105 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8318 (tt) REVERT: C 112 GLN cc_start: 0.7660 (tt0) cc_final: 0.7266 (tp40) REVERT: C 210 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: C 273 MET cc_start: 0.8285 (tpp) cc_final: 0.7765 (tpp) REVERT: D 54 ARG cc_start: 0.7135 (mtp180) cc_final: 0.6760 (mtp180) REVERT: E 20 ASN cc_start: 0.2550 (OUTLIER) cc_final: 0.1347 (p0) REVERT: E 35 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8322 (mm) REVERT: E 210 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: F 273 MET cc_start: 0.8426 (ttm) cc_final: 0.7901 (ttm) REVERT: G 210 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: G 278 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7009 (mtmt) outliers start: 30 outliers final: 8 residues processed: 229 average time/residue: 1.8399 time to fit residues: 451.0235 Evaluate side-chains 226 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 278 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 149 GLN D 92 GLN F 112 GLN F 149 GLN G 30 ASN G 53 ASN G 149 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15813 Z= 0.178 Angle : 0.451 4.556 21301 Z= 0.239 Chirality : 0.040 0.148 2681 Planarity : 0.003 0.039 2450 Dihedral : 13.832 123.848 4459 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 1.75 % Allowed : 13.95 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.18), residues: 1820 helix: 3.21 (0.15), residues: 1029 sheet: 0.22 (0.27), residues: 280 loop : -0.72 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 251 PHE 0.014 0.002 PHE B 178 TYR 0.009 0.001 TYR B 75 ARG 0.009 0.000 ARG C 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.525 Fit side-chains REVERT: A 105 LEU cc_start: 0.8808 (tp) cc_final: 0.8589 (tp) REVERT: A 112 GLN cc_start: 0.7600 (tt0) cc_final: 0.7357 (tt0) REVERT: A 210 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: B 210 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: C 20 ASN cc_start: 0.1942 (OUTLIER) cc_final: 0.1724 (p0) REVERT: C 61 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8369 (mt) REVERT: C 112 GLN cc_start: 0.7674 (tt0) cc_final: 0.7292 (tp40) REVERT: C 210 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7691 (mp10) REVERT: C 273 MET cc_start: 0.8318 (tpp) cc_final: 0.7745 (tpp) REVERT: D 54 ARG cc_start: 0.7116 (mtp180) cc_final: 0.6774 (mtp180) REVERT: E 20 ASN cc_start: 0.2621 (OUTLIER) cc_final: 0.1399 (p0) REVERT: E 35 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8337 (mm) REVERT: E 210 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: F 20 ASN cc_start: 0.1903 (OUTLIER) cc_final: 0.0589 (p0) REVERT: F 273 MET cc_start: 0.8399 (ttm) cc_final: 0.7878 (ttm) REVERT: G 20 ASN cc_start: 0.2737 (OUTLIER) cc_final: 0.2207 (p0) REVERT: G 210 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: G 278 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7019 (mtmt) outliers start: 26 outliers final: 8 residues processed: 227 average time/residue: 1.9477 time to fit residues: 474.9988 Evaluate side-chains 228 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 210 GLN Chi-restraints excluded: chain G residue 278 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 21 optimal weight: 0.0570 chunk 40 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN F 112 GLN F 149 GLN G 149 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.117735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.092005 restraints weight = 17632.209| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.13 r_work: 0.2747 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15813 Z= 0.132 Angle : 0.421 4.586 21301 Z= 0.225 Chirality : 0.040 0.143 2681 Planarity : 0.003 0.039 2450 Dihedral : 13.577 124.182 4459 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 1.75 % Allowed : 13.75 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.18), residues: 1820 helix: 3.31 (0.15), residues: 1029 sheet: 0.18 (0.27), residues: 280 loop : -0.74 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 251 PHE 0.011 0.001 PHE B 178 TYR 0.007 0.001 TYR B 75 ARG 0.009 0.000 ARG C 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6817.44 seconds wall clock time: 119 minutes 22.97 seconds (7162.97 seconds total)