Starting phenix.real_space_refine on Wed Apr 30 11:41:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jr3_61747/04_2025/9jr3_61747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jr3_61747/04_2025/9jr3_61747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jr3_61747/04_2025/9jr3_61747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jr3_61747/04_2025/9jr3_61747.map" model { file = "/net/cci-nas-00/data/ceres_data/9jr3_61747/04_2025/9jr3_61747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jr3_61747/04_2025/9jr3_61747.cif" } resolution = 2.8 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 ------------------------------------------------------------------------------- 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= 1.572 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 60 5.16 5 C 6056 2.51 5 N 1618 2.21 5 O 1721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 9455 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2865 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 345} Chain breaks: 5 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "P" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1722 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2473 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1727 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" 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: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.16, per 1000 atoms: 0.65 Number of scatterers: 9455 At special positions: 0 Unit cell: (84.624, 123, 161.868, 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 60 16.00 O 1721 8.00 N 1618 7.00 C 6056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 176 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2302 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 39.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'R' and resid 33 through 54 Processing helix chain 'R' and resid 176 through 212 removed outlier: 3.553A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 removed outlier: 3.539A pdb=" N HIS R 216 " --> pdb=" O ARG R 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 213 through 216' Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 279 through 312 removed outlier: 3.859A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 347 removed outlier: 3.924A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.711A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 removed outlier: 4.021A pdb=" N LYS R 405 " --> pdb=" O GLN R 401 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 Processing helix chain 'R' and resid 434 through 450 removed outlier: 3.547A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) Processing helix chain 'R' and resid 450 through 459 Processing helix chain 'R' and resid 463 through 482 Processing helix chain 'P' and resid 2 through 17 removed outlier: 3.505A pdb=" N LYS P 13 " --> pdb=" O HIS P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 34 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.771A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.934A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 183 through 202 Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.609A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.681A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.919A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.095A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.617A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 126 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 76 removed outlier: 7.122A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.200A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.897A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.843A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.655A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.036A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.496A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.592A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.713A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.714A pdb=" N ARG S 148 " --> pdb=" O THR S 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 135 through 136 removed outlier: 3.921A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 146 493 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3031 1.34 - 1.46: 2489 1.46 - 1.58: 4065 1.58 - 1.70: 0 1.70 - 1.81: 86 Bond restraints: 9671 Sorted by residual: bond pdb=" N LEU B 4 " pdb=" CA LEU B 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N GLN G 11 " pdb=" CA GLN G 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N VAL S 2 " pdb=" CA VAL S 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N VAL A 5 " pdb=" CA VAL A 5 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N PHE P 34 " pdb=" CA PHE P 34 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 ... (remaining 9666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 12626 1.09 - 2.18: 437 2.18 - 3.26: 48 3.26 - 4.35: 30 4.35 - 5.44: 2 Bond angle restraints: 13143 Sorted by residual: angle pdb=" C LYS A 95 " pdb=" N TRP A 96 " pdb=" CA TRP A 96 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.11e+00 angle pdb=" N PRO A 180 " pdb=" CA PRO A 180 " pdb=" C PRO A 180 " ideal model delta sigma weight residual 114.92 111.63 3.29 1.19e+00 7.06e-01 7.66e+00 angle pdb=" CA ILE R 310 " pdb=" C ILE R 310 " pdb=" N PHE R 311 " ideal model delta sigma weight residual 116.60 119.88 -3.28 1.45e+00 4.76e-01 5.12e+00 angle pdb=" CA SER S 181 " pdb=" C SER S 181 " pdb=" N ASN S 182 " ideal model delta sigma weight residual 116.84 120.59 -3.75 1.71e+00 3.42e-01 4.80e+00 angle pdb=" N TRP A 96 " pdb=" CA TRP A 96 " pdb=" C TRP A 96 " ideal model delta sigma weight residual 110.80 106.52 4.28 2.13e+00 2.20e-01 4.05e+00 ... (remaining 13138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 5048 16.06 - 32.12: 459 32.12 - 48.18: 121 48.18 - 64.25: 34 64.25 - 80.31: 6 Dihedral angle restraints: 5668 sinusoidal: 2103 harmonic: 3565 Sorted by residual: dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 117 " pdb=" CB CYS R 117 " ideal model delta sinusoidal sigma weight residual -86.00 -158.47 72.47 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CA ASP A 199 " pdb=" C ASP A 199 " pdb=" N ILE A 200 " pdb=" CA ILE A 200 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 60.42 32.58 1 1.00e+01 1.00e-02 1.51e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1091 0.036 - 0.073: 298 0.073 - 0.109: 78 0.109 - 0.146: 25 0.146 - 0.182: 1 Chirality restraints: 1493 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 9.71e-01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN R 176 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1490 not shown) Planarity restraints: 1657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO S 107 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO G 49 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 172 " 0.026 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO S 173 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO S 173 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO S 173 " 0.022 5.00e-02 4.00e+02 ... (remaining 1654 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 194 2.69 - 3.24: 9256 3.24 - 3.79: 14973 3.79 - 4.35: 20611 4.35 - 4.90: 33906 Nonbonded interactions: 78940 Sorted by model distance: nonbonded pdb=" O GLU R 302 " pdb=" O HOH R 601 " model vdw 2.136 3.040 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.192 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O GLY B 288 " model vdw 2.260 3.040 nonbonded pdb=" O SER R 341 " pdb=" OG1 THR R 345 " model vdw 2.303 3.040 ... (remaining 78935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 21.560 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: 0.800 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.660 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 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 : 0.003 0.107 9680 Z= 0.169 Angle : 0.491 5.440 13161 Z= 0.277 Chirality : 0.039 0.182 1493 Planarity : 0.004 0.052 1656 Dihedral : 13.980 80.306 3348 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 0.62 % Allowed : 11.95 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.36 (0.25), residues: 1200 helix: 1.51 (0.26), residues: 436 sheet: -0.33 (0.32), residues: 259 loop : -0.49 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 298 HIS 0.005 0.001 HIS P 14 PHE 0.009 0.001 PHE R 335 TYR 0.009 0.001 TYR R 191 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 1) link_NAG-ASN : angle 0.73955 ( 3) link_BETA1-4 : bond 0.00207 ( 1) link_BETA1-4 : angle 1.27680 ( 3) hydrogen bonds : bond 0.17874 ( 493) hydrogen bonds : angle 6.60418 ( 1374) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.46721 ( 12) covalent geometry : bond 0.00262 ( 9671) covalent geometry : angle 0.49068 (13143) Misc. bond : bond 0.10668 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 1.068 Fit side-chains REVERT: R 32 MET cc_start: 0.5891 (mtp) cc_final: 0.5020 (ttm) REVERT: R 189 MET cc_start: 0.6155 (mmm) cc_final: 0.5929 (mmm) REVERT: R 201 SER cc_start: 0.6297 (m) cc_final: 0.6072 (p) REVERT: R 213 ARG cc_start: 0.6087 (mtt180) cc_final: 0.5485 (mtp180) REVERT: R 214 ARG cc_start: 0.5921 (mmm160) cc_final: 0.5691 (mmm-85) REVERT: R 231 MET cc_start: 0.7273 (mtp) cc_final: 0.7020 (mtm) REVERT: R 312 MET cc_start: 0.5307 (mmm) cc_final: 0.4925 (mtp) REVERT: R 431 GLU cc_start: 0.6475 (tt0) cc_final: 0.6017 (tt0) REVERT: R 438 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6655 (mm-40) REVERT: R 455 VAL cc_start: 0.7784 (t) cc_final: 0.7520 (m) REVERT: P 8 MET cc_start: 0.6380 (ttp) cc_final: 0.6174 (ttp) REVERT: A 14 GLU cc_start: 0.5639 (tt0) cc_final: 0.5289 (mt-10) REVERT: A 17 LYS cc_start: 0.4326 (mttm) cc_final: 0.3643 (mtpt) REVERT: A 21 LYS cc_start: 0.4484 (tttm) cc_final: 0.3749 (mmpt) REVERT: A 73 LYS cc_start: 0.5898 (mttp) cc_final: 0.5235 (pmtt) REVERT: A 103 VAL cc_start: 0.7336 (t) cc_final: 0.7078 (p) REVERT: A 126 LYS cc_start: 0.4865 (ttmt) cc_final: 0.4039 (pptt) REVERT: A 188 ARG cc_start: 0.3888 (ttp80) cc_final: 0.3628 (ptm160) REVERT: A 196 GLU cc_start: 0.3461 (mm-30) cc_final: 0.2714 (mm-30) REVERT: A 238 MET cc_start: 0.6154 (mtm) cc_final: 0.5602 (ptm) REVERT: A 241 ARG cc_start: 0.6556 (ttm-80) cc_final: 0.6339 (mtm-85) REVERT: B 78 LYS cc_start: 0.6642 (ttmm) cc_final: 0.6353 (tppt) REVERT: B 98 SER cc_start: 0.7454 (p) cc_final: 0.7233 (p) REVERT: B 137 ARG cc_start: 0.4929 (tpp-160) cc_final: 0.4350 (tpt90) REVERT: B 146 LEU cc_start: 0.7948 (mt) cc_final: 0.7393 (tp) REVERT: B 177 THR cc_start: 0.7772 (m) cc_final: 0.7414 (p) REVERT: B 219 ARG cc_start: 0.6830 (mtp180) cc_final: 0.6557 (mmt-90) REVERT: B 277 SER cc_start: 0.7749 (t) cc_final: 0.7102 (m) REVERT: B 285 LEU cc_start: 0.6636 (tp) cc_final: 0.6323 (tm) REVERT: B 325 MET cc_start: 0.6274 (tpp) cc_final: 0.5947 (tpp) REVERT: S 18 ARG cc_start: 0.4421 (ttm-80) cc_final: 0.4199 (ttt90) REVERT: S 222 GLU cc_start: 0.6506 (pt0) cc_final: 0.5712 (mm-30) outliers start: 6 outliers final: 1 residues processed: 197 average time/residue: 1.1976 time to fit residues: 253.4162 Evaluate side-chains 151 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 387 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 47 GLN R 216 HIS R 225 HIS ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 442 HIS P 6 GLN A 43 ASN A 229 ASN B 32 GLN B 35 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 239 ASN B 268 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.211879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.172789 restraints weight = 10311.947| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.65 r_work: 0.3792 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 9680 Z= 0.256 Angle : 0.671 8.028 13161 Z= 0.357 Chirality : 0.047 0.179 1493 Planarity : 0.005 0.057 1656 Dihedral : 4.886 30.086 1367 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.08 % Favored : 96.83 % Rotamer: Outliers : 3.53 % Allowed : 16.01 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.31 (0.24), residues: 1200 helix: 1.33 (0.24), residues: 442 sheet: -0.20 (0.32), residues: 271 loop : -0.51 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.007 0.002 HIS R 442 PHE 0.022 0.002 PHE A 215 TYR 0.016 0.002 TYR R 297 ARG 0.004 0.001 ARG A 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 1) link_NAG-ASN : angle 1.77994 ( 3) link_BETA1-4 : bond 0.01142 ( 1) link_BETA1-4 : angle 0.86938 ( 3) hydrogen bonds : bond 0.05992 ( 493) hydrogen bonds : angle 5.10540 ( 1374) SS BOND : bond 0.00747 ( 6) SS BOND : angle 1.12720 ( 12) covalent geometry : bond 0.00597 ( 9671) covalent geometry : angle 0.66975 (13143) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.972 Fit side-chains REVERT: R 32 MET cc_start: 0.6165 (mtp) cc_final: 0.5905 (ttm) REVERT: A 17 LYS cc_start: 0.6839 (mttm) cc_final: 0.6065 (mtmt) REVERT: A 21 LYS cc_start: 0.6361 (tttm) cc_final: 0.5645 (mmpt) REVERT: A 43 ASN cc_start: 0.5411 (OUTLIER) cc_final: 0.4698 (m-40) REVERT: A 73 LYS cc_start: 0.5981 (mttp) cc_final: 0.5551 (pmtt) REVERT: A 126 LYS cc_start: 0.6280 (ttmt) cc_final: 0.5324 (pptt) REVERT: A 196 GLU cc_start: 0.5061 (mm-30) cc_final: 0.4081 (mm-30) REVERT: A 246 VAL cc_start: 0.7313 (OUTLIER) cc_final: 0.6885 (t) REVERT: B 78 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8253 (tppt) REVERT: B 146 LEU cc_start: 0.8273 (mt) cc_final: 0.7980 (tp) REVERT: B 175 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7695 (mp10) REVERT: S 198 THR cc_start: 0.4544 (OUTLIER) cc_final: 0.4144 (p) outliers start: 34 outliers final: 15 residues processed: 175 average time/residue: 1.0920 time to fit residues: 206.0715 Evaluate side-chains 158 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 435 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 120 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.213526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.174880 restraints weight = 10370.827| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.61 r_work: 0.3826 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9680 Z= 0.155 Angle : 0.564 7.957 13161 Z= 0.302 Chirality : 0.043 0.165 1493 Planarity : 0.004 0.054 1656 Dihedral : 4.638 29.436 1367 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.42 % Rotamer: Outliers : 4.26 % Allowed : 17.98 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.51 (0.24), residues: 1200 helix: 1.66 (0.24), residues: 446 sheet: -0.12 (0.32), residues: 260 loop : -0.57 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 96 HIS 0.004 0.001 HIS A 209 PHE 0.015 0.002 PHE R 335 TYR 0.014 0.001 TYR R 191 ARG 0.008 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 1) link_NAG-ASN : angle 2.09775 ( 3) link_BETA1-4 : bond 0.00802 ( 1) link_BETA1-4 : angle 0.69116 ( 3) hydrogen bonds : bond 0.04809 ( 493) hydrogen bonds : angle 4.74160 ( 1374) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.73611 ( 12) covalent geometry : bond 0.00350 ( 9671) covalent geometry : angle 0.56304 (13143) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 1.037 Fit side-chains REVERT: R 32 MET cc_start: 0.6225 (mtp) cc_final: 0.5845 (ttm) REVERT: R 115 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7318 (mp) REVERT: A 17 LYS cc_start: 0.6659 (mttm) cc_final: 0.5951 (mtpt) REVERT: A 21 LYS cc_start: 0.6349 (tttm) cc_final: 0.5672 (mmpt) REVERT: A 43 ASN cc_start: 0.5409 (OUTLIER) cc_final: 0.4576 (m-40) REVERT: A 73 LYS cc_start: 0.5839 (mttp) cc_final: 0.5465 (pttt) REVERT: A 126 LYS cc_start: 0.6285 (ttmt) cc_final: 0.5292 (pptt) REVERT: A 188 ARG cc_start: 0.5190 (ptm160) cc_final: 0.4904 (ptm160) REVERT: A 196 GLU cc_start: 0.4967 (mm-30) cc_final: 0.3954 (mm-30) REVERT: B 78 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8171 (tppt) REVERT: B 146 LEU cc_start: 0.8177 (mt) cc_final: 0.7957 (tp) REVERT: S 198 THR cc_start: 0.4367 (OUTLIER) cc_final: 0.3955 (p) REVERT: S 222 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6890 (mt-10) outliers start: 41 outliers final: 18 residues processed: 165 average time/residue: 1.1712 time to fit residues: 207.3625 Evaluate side-chains 156 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 92 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 24 optimal weight: 0.0370 chunk 62 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 96 optimal weight: 0.0030 chunk 13 optimal weight: 4.9990 overall best weight: 1.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN A 43 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.213152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174363 restraints weight = 10261.919| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.62 r_work: 0.3834 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9680 Z= 0.143 Angle : 0.547 8.221 13161 Z= 0.293 Chirality : 0.042 0.161 1493 Planarity : 0.004 0.051 1656 Dihedral : 4.456 25.824 1366 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.42 % Rotamer: Outliers : 4.68 % Allowed : 17.05 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.61 (0.24), residues: 1200 helix: 1.80 (0.24), residues: 447 sheet: -0.10 (0.32), residues: 260 loop : -0.55 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 96 HIS 0.004 0.001 HIS A 209 PHE 0.016 0.001 PHE R 335 TYR 0.034 0.001 TYR R 191 ARG 0.009 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 1) link_NAG-ASN : angle 2.04014 ( 3) link_BETA1-4 : bond 0.00773 ( 1) link_BETA1-4 : angle 0.70127 ( 3) hydrogen bonds : bond 0.04486 ( 493) hydrogen bonds : angle 4.60269 ( 1374) SS BOND : bond 0.00483 ( 6) SS BOND : angle 0.65688 ( 12) covalent geometry : bond 0.00321 ( 9671) covalent geometry : angle 0.54631 (13143) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.971 Fit side-chains REVERT: R 32 MET cc_start: 0.6153 (mtp) cc_final: 0.5759 (ttm) REVERT: R 115 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7381 (mp) REVERT: A 17 LYS cc_start: 0.6614 (mttm) cc_final: 0.5897 (mtpt) REVERT: A 21 LYS cc_start: 0.6291 (tttm) cc_final: 0.5619 (mmpt) REVERT: A 43 ASN cc_start: 0.5438 (OUTLIER) cc_final: 0.4375 (t0) REVERT: A 126 LYS cc_start: 0.6255 (ttmt) cc_final: 0.5201 (pptt) REVERT: A 196 GLU cc_start: 0.4869 (mm-30) cc_final: 0.3885 (mm-30) REVERT: B 78 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8095 (tppt) REVERT: B 146 LEU cc_start: 0.8183 (mt) cc_final: 0.7967 (tp) REVERT: S 128 MET cc_start: 0.5598 (mpp) cc_final: 0.5317 (mpt) REVERT: S 180 MET cc_start: 0.6080 (tpt) cc_final: 0.5720 (tpt) REVERT: S 192 SER cc_start: 0.7338 (t) cc_final: 0.7070 (m) REVERT: S 198 THR cc_start: 0.4318 (OUTLIER) cc_final: 0.3905 (p) REVERT: S 222 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6860 (mt-10) outliers start: 45 outliers final: 24 residues processed: 173 average time/residue: 1.2094 time to fit residues: 225.8947 Evaluate side-chains 166 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 116 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 63 optimal weight: 0.3980 chunk 11 optimal weight: 0.0970 chunk 49 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 115 optimal weight: 0.0570 chunk 2 optimal weight: 10.0000 overall best weight: 0.7216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.216156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.178003 restraints weight = 10368.598| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.63 r_work: 0.3863 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9680 Z= 0.110 Angle : 0.507 7.442 13161 Z= 0.271 Chirality : 0.041 0.157 1493 Planarity : 0.004 0.048 1656 Dihedral : 4.186 25.976 1366 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.83 % Rotamer: Outliers : 3.95 % Allowed : 18.92 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.85 (0.25), residues: 1200 helix: 2.08 (0.24), residues: 447 sheet: 0.04 (0.32), residues: 258 loop : -0.52 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 96 HIS 0.004 0.001 HIS A 209 PHE 0.017 0.001 PHE R 335 TYR 0.015 0.001 TYR R 191 ARG 0.008 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 1) link_NAG-ASN : angle 2.07766 ( 3) link_BETA1-4 : bond 0.00729 ( 1) link_BETA1-4 : angle 0.78484 ( 3) hydrogen bonds : bond 0.03950 ( 493) hydrogen bonds : angle 4.35974 ( 1374) SS BOND : bond 0.00142 ( 6) SS BOND : angle 0.58838 ( 12) covalent geometry : bond 0.00236 ( 9671) covalent geometry : angle 0.50628 (13143) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.992 Fit side-chains REVERT: R 32 MET cc_start: 0.6075 (mtp) cc_final: 0.5688 (ttm) REVERT: R 115 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7358 (mp) REVERT: R 180 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6229 (mt-10) REVERT: A 17 LYS cc_start: 0.6552 (mttm) cc_final: 0.5872 (mtpt) REVERT: A 43 ASN cc_start: 0.5555 (OUTLIER) cc_final: 0.4154 (t0) REVERT: A 126 LYS cc_start: 0.6277 (ttmt) cc_final: 0.5267 (pptt) REVERT: A 196 GLU cc_start: 0.4809 (mm-30) cc_final: 0.3839 (mm-30) REVERT: B 146 LEU cc_start: 0.8135 (mt) cc_final: 0.7928 (tp) REVERT: B 252 LEU cc_start: 0.7345 (tt) cc_final: 0.7062 (tp) REVERT: S 83 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6765 (mtt) REVERT: S 128 MET cc_start: 0.5602 (mpp) cc_final: 0.5385 (mpt) REVERT: S 180 MET cc_start: 0.6020 (tpt) cc_final: 0.5671 (tpt) REVERT: S 192 SER cc_start: 0.7325 (t) cc_final: 0.7075 (m) REVERT: S 198 THR cc_start: 0.4225 (OUTLIER) cc_final: 0.3831 (p) REVERT: S 222 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6842 (mt-10) outliers start: 38 outliers final: 18 residues processed: 155 average time/residue: 1.3926 time to fit residues: 231.3618 Evaluate side-chains 154 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 8 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.211071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.171919 restraints weight = 10291.137| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.64 r_work: 0.3807 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9680 Z= 0.181 Angle : 0.578 7.721 13161 Z= 0.306 Chirality : 0.043 0.157 1493 Planarity : 0.004 0.049 1656 Dihedral : 4.482 25.745 1366 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 4.37 % Allowed : 18.30 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.70 (0.24), residues: 1200 helix: 1.91 (0.24), residues: 447 sheet: -0.11 (0.32), residues: 260 loop : -0.50 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS S 155 PHE 0.019 0.002 PHE R 453 TYR 0.017 0.002 TYR R 191 ARG 0.010 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 1) link_NAG-ASN : angle 1.93338 ( 3) link_BETA1-4 : bond 0.00564 ( 1) link_BETA1-4 : angle 0.86528 ( 3) hydrogen bonds : bond 0.04606 ( 493) hydrogen bonds : angle 4.59444 ( 1374) SS BOND : bond 0.00239 ( 6) SS BOND : angle 0.59299 ( 12) covalent geometry : bond 0.00422 ( 9671) covalent geometry : angle 0.57743 (13143) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 1.110 Fit side-chains REVERT: R 32 MET cc_start: 0.6078 (mtp) cc_final: 0.5787 (ttm) REVERT: R 115 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7383 (mp) REVERT: A 10 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7421 (ttpt) REVERT: A 17 LYS cc_start: 0.6633 (mmtm) cc_final: 0.5890 (mtpt) REVERT: A 21 LYS cc_start: 0.6359 (tttm) cc_final: 0.5642 (mmpt) REVERT: A 22 ASN cc_start: 0.6856 (m-40) cc_final: 0.6530 (m-40) REVERT: A 43 ASN cc_start: 0.5830 (OUTLIER) cc_final: 0.4121 (t0) REVERT: A 126 LYS cc_start: 0.6275 (ttmt) cc_final: 0.5219 (pptt) REVERT: A 196 GLU cc_start: 0.4874 (mm-30) cc_final: 0.3842 (mm-30) REVERT: B 252 LEU cc_start: 0.7503 (tt) cc_final: 0.7203 (tp) REVERT: S 128 MET cc_start: 0.5730 (mpp) cc_final: 0.5474 (mpt) REVERT: S 192 SER cc_start: 0.7299 (t) cc_final: 0.7037 (m) REVERT: S 198 THR cc_start: 0.4305 (OUTLIER) cc_final: 0.3911 (p) REVERT: S 222 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6868 (mt-10) outliers start: 42 outliers final: 23 residues processed: 157 average time/residue: 1.1415 time to fit residues: 193.2335 Evaluate side-chains 162 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 56 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 100 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 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 = 0.4325 r_free = 0.4325 target = 0.213606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175326 restraints weight = 10377.464| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.62 r_work: 0.3817 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9680 Z= 0.132 Angle : 0.533 7.314 13161 Z= 0.285 Chirality : 0.041 0.158 1493 Planarity : 0.004 0.047 1656 Dihedral : 4.350 25.760 1366 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.42 % Rotamer: Outliers : 4.26 % Allowed : 19.13 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.81 (0.25), residues: 1200 helix: 2.02 (0.24), residues: 447 sheet: -0.02 (0.32), residues: 258 loop : -0.48 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.020 0.001 PHE B 241 TYR 0.015 0.001 TYR R 191 ARG 0.009 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 1) link_NAG-ASN : angle 2.03189 ( 3) link_BETA1-4 : bond 0.00926 ( 1) link_BETA1-4 : angle 0.84589 ( 3) hydrogen bonds : bond 0.04154 ( 493) hydrogen bonds : angle 4.45794 ( 1374) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.57782 ( 12) covalent geometry : bond 0.00298 ( 9671) covalent geometry : angle 0.53223 (13143) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 1.049 Fit side-chains REVERT: R 32 MET cc_start: 0.5990 (mtp) cc_final: 0.5778 (ttm) REVERT: R 115 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7391 (mp) REVERT: A 10 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7370 (ttpt) REVERT: A 17 LYS cc_start: 0.6578 (mmtm) cc_final: 0.5869 (mtpt) REVERT: A 126 LYS cc_start: 0.6240 (ttmt) cc_final: 0.5219 (pptt) REVERT: A 196 GLU cc_start: 0.4810 (mm-30) cc_final: 0.3795 (mm-30) REVERT: B 252 LEU cc_start: 0.7416 (tt) cc_final: 0.7126 (tp) REVERT: S 67 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6645 (mtm180) REVERT: S 128 MET cc_start: 0.5700 (mpp) cc_final: 0.5474 (mpt) REVERT: S 180 MET cc_start: 0.6035 (tpt) cc_final: 0.5723 (tpt) REVERT: S 192 SER cc_start: 0.7298 (t) cc_final: 0.7022 (m) REVERT: S 198 THR cc_start: 0.4241 (OUTLIER) cc_final: 0.3838 (p) REVERT: S 222 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6877 (mt-10) outliers start: 41 outliers final: 26 residues processed: 156 average time/residue: 1.2149 time to fit residues: 203.8096 Evaluate side-chains 163 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 64 optimal weight: 0.3980 chunk 46 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 108 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 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 = 0.4334 r_free = 0.4334 target = 0.214594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176581 restraints weight = 10529.517| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.63 r_work: 0.3846 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9680 Z= 0.119 Angle : 0.522 7.045 13161 Z= 0.278 Chirality : 0.041 0.157 1493 Planarity : 0.004 0.046 1656 Dihedral : 4.237 25.974 1366 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Rotamer: Outliers : 4.05 % Allowed : 19.54 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1200 helix: 2.10 (0.24), residues: 447 sheet: 0.01 (0.33), residues: 240 loop : -0.41 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.019 0.001 PHE B 241 TYR 0.012 0.001 TYR R 191 ARG 0.010 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 1) link_NAG-ASN : angle 2.02847 ( 3) link_BETA1-4 : bond 0.00604 ( 1) link_BETA1-4 : angle 0.87085 ( 3) hydrogen bonds : bond 0.03961 ( 493) hydrogen bonds : angle 4.36825 ( 1374) SS BOND : bond 0.00147 ( 6) SS BOND : angle 0.54314 ( 12) covalent geometry : bond 0.00264 ( 9671) covalent geometry : angle 0.52100 (13143) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 1.047 Fit side-chains REVERT: R 32 MET cc_start: 0.5936 (mtp) cc_final: 0.5727 (ttm) REVERT: R 115 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7416 (mp) REVERT: A 17 LYS cc_start: 0.6583 (mmtm) cc_final: 0.5872 (mtpt) REVERT: A 22 ASN cc_start: 0.6782 (m-40) cc_final: 0.6541 (m-40) REVERT: A 126 LYS cc_start: 0.6263 (ttmt) cc_final: 0.5243 (pptt) REVERT: A 196 GLU cc_start: 0.4817 (mm-30) cc_final: 0.3808 (mm-30) REVERT: B 252 LEU cc_start: 0.7401 (tt) cc_final: 0.7098 (tp) REVERT: S 67 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6714 (mtm180) REVERT: S 180 MET cc_start: 0.6037 (tpt) cc_final: 0.5708 (tpt) REVERT: S 192 SER cc_start: 0.7282 (t) cc_final: 0.7070 (m) REVERT: S 198 THR cc_start: 0.4204 (OUTLIER) cc_final: 0.3791 (p) REVERT: S 222 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6885 (mt-10) outliers start: 39 outliers final: 25 residues processed: 159 average time/residue: 1.1909 time to fit residues: 204.0975 Evaluate side-chains 166 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 179 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 28 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 43 optimal weight: 0.0050 chunk 35 optimal weight: 0.4980 chunk 71 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 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 = 0.4353 r_free = 0.4353 target = 0.216928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.179333 restraints weight = 10442.497| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.63 r_work: 0.3886 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9680 Z= 0.100 Angle : 0.506 10.418 13161 Z= 0.267 Chirality : 0.041 0.155 1493 Planarity : 0.004 0.045 1656 Dihedral : 4.014 26.479 1366 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.83 % Rotamer: Outliers : 3.01 % Allowed : 21.00 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1200 helix: 2.30 (0.25), residues: 447 sheet: 0.28 (0.32), residues: 249 loop : -0.45 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.006 0.001 HIS S 155 PHE 0.018 0.001 PHE B 241 TYR 0.025 0.001 TYR R 191 ARG 0.011 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 1) link_NAG-ASN : angle 1.95226 ( 3) link_BETA1-4 : bond 0.00673 ( 1) link_BETA1-4 : angle 0.91291 ( 3) hydrogen bonds : bond 0.03563 ( 493) hydrogen bonds : angle 4.18978 ( 1374) SS BOND : bond 0.00111 ( 6) SS BOND : angle 0.53386 ( 12) covalent geometry : bond 0.00214 ( 9671) covalent geometry : angle 0.50546 (13143) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: R 32 MET cc_start: 0.5793 (mtp) cc_final: 0.5587 (ttm) REVERT: R 115 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7438 (mp) REVERT: R 213 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7203 (tpt90) REVERT: A 17 LYS cc_start: 0.6516 (mmtm) cc_final: 0.5784 (mtpt) REVERT: A 126 LYS cc_start: 0.6269 (ttmt) cc_final: 0.5269 (pptt) REVERT: A 196 GLU cc_start: 0.4613 (mm-30) cc_final: 0.3659 (mm-30) REVERT: B 252 LEU cc_start: 0.7344 (tt) cc_final: 0.7066 (tp) REVERT: S 180 MET cc_start: 0.5941 (tpt) cc_final: 0.5670 (tpt) REVERT: S 198 THR cc_start: 0.4213 (OUTLIER) cc_final: 0.3832 (p) outliers start: 29 outliers final: 20 residues processed: 156 average time/residue: 1.2496 time to fit residues: 209.5808 Evaluate side-chains 155 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 11 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 0.0040 chunk 119 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN P 6 GLN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.217110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.179621 restraints weight = 10513.922| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.61 r_work: 0.3878 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9680 Z= 0.106 Angle : 0.513 7.460 13161 Z= 0.272 Chirality : 0.041 0.165 1493 Planarity : 0.004 0.045 1656 Dihedral : 4.025 26.273 1366 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.60 % Allowed : 21.52 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1200 helix: 2.31 (0.25), residues: 447 sheet: 0.17 (0.33), residues: 237 loop : -0.38 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.022 0.001 PHE R 453 TYR 0.016 0.001 TYR R 191 ARG 0.011 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 1.70084 ( 3) link_BETA1-4 : bond 0.00632 ( 1) link_BETA1-4 : angle 0.91339 ( 3) hydrogen bonds : bond 0.03643 ( 493) hydrogen bonds : angle 4.16468 ( 1374) SS BOND : bond 0.00127 ( 6) SS BOND : angle 0.88000 ( 12) covalent geometry : bond 0.00233 ( 9671) covalent geometry : angle 0.51199 (13143) Misc. bond : bond 0.00005 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 3.402 Fit side-chains revert: symmetry clash REVERT: R 115 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7468 (mp) REVERT: R 213 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7220 (tpt90) REVERT: A 17 LYS cc_start: 0.6492 (mmtm) cc_final: 0.5787 (mtmt) REVERT: A 126 LYS cc_start: 0.6287 (ttmt) cc_final: 0.5295 (pptt) REVERT: A 196 GLU cc_start: 0.4646 (mm-30) cc_final: 0.3667 (mm-30) REVERT: B 252 LEU cc_start: 0.7357 (tt) cc_final: 0.7084 (tp) REVERT: S 180 MET cc_start: 0.5931 (tpt) cc_final: 0.5516 (tpt) REVERT: S 198 THR cc_start: 0.4199 (OUTLIER) cc_final: 0.3805 (p) outliers start: 25 outliers final: 18 residues processed: 145 average time/residue: 1.4115 time to fit residues: 221.6919 Evaluate side-chains 145 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 177 GLU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 102 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.211829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.172896 restraints weight = 10273.721| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.62 r_work: 0.3812 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9680 Z= 0.195 Angle : 0.615 9.913 13161 Z= 0.322 Chirality : 0.044 0.169 1493 Planarity : 0.004 0.047 1656 Dihedral : 4.518 25.782 1366 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 3.22 % Allowed : 21.31 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.82 (0.24), residues: 1200 helix: 1.93 (0.24), residues: 446 sheet: 0.06 (0.32), residues: 261 loop : -0.42 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 82 HIS 0.009 0.002 HIS S 155 PHE 0.022 0.002 PHE B 241 TYR 0.016 0.002 TYR R 297 ARG 0.010 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 1) link_NAG-ASN : angle 1.63475 ( 3) link_BETA1-4 : bond 0.00748 ( 1) link_BETA1-4 : angle 0.97511 ( 3) hydrogen bonds : bond 0.04620 ( 493) hydrogen bonds : angle 4.55569 ( 1374) SS BOND : bond 0.00276 ( 6) SS BOND : angle 1.06523 ( 12) covalent geometry : bond 0.00454 ( 9671) covalent geometry : angle 0.61375 (13143) Misc. bond : bond 0.00024 ( 1) =============================================================================== Job complete usr+sys time: 9967.59 seconds wall clock time: 175 minutes 36.25 seconds (10536.25 seconds total)