Starting phenix.real_space_refine on Tue May 13 00:02:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jr3_61747/05_2025/9jr3_61747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jr3_61747/05_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_61747/05_2025/9jr3_61747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jr3_61747/05_2025/9jr3_61747.map" model { file = "/net/cci-nas-00/data/ceres_data/9jr3_61747/05_2025/9jr3_61747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jr3_61747/05_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-5687/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: 6.12, 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: 2.55 Conformation dependent library (CDL) restraints added in 1.0 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: 0.95 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: 2.69 Time building geometry restraints manager: 2.94 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: 4.980 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: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.630 Find NCS groups from input model: 0.100 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.380 ------------------------------------------------------------------------------- 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 : 1.061 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: 1.1424 time to fit residues: 241.7398 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 : 1.102 ------------------------------------------------------------------------------- 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 = 0.211878 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: 2.52 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- 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 0.86939 ( 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 : 1.040 Fit side-chains REVERT: R 32 MET cc_start: 0.6159 (mtp) cc_final: 0.5898 (ttm) REVERT: A 17 LYS cc_start: 0.6837 (mttm) cc_final: 0.6065 (mtmt) REVERT: A 21 LYS cc_start: 0.6360 (tttm) cc_final: 0.5646 (mmpt) REVERT: A 43 ASN cc_start: 0.5412 (OUTLIER) cc_final: 0.4697 (m-40) REVERT: A 73 LYS cc_start: 0.5979 (mttp) cc_final: 0.5552 (pmtt) REVERT: A 126 LYS cc_start: 0.6276 (ttmt) cc_final: 0.5322 (pptt) REVERT: A 196 GLU cc_start: 0.5061 (mm-30) cc_final: 0.4080 (mm-30) REVERT: A 246 VAL cc_start: 0.7315 (OUTLIER) cc_final: 0.6885 (t) REVERT: B 78 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8254 (tppt) REVERT: B 146 LEU cc_start: 0.8271 (mt) cc_final: 0.7979 (tp) REVERT: B 175 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7697 (mp10) REVERT: S 198 THR cc_start: 0.4545 (OUTLIER) cc_final: 0.4144 (p) outliers start: 34 outliers final: 15 residues processed: 175 average time/residue: 1.0665 time to fit residues: 201.2596 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 : 0.974 ------------------------------------------------------------------------------- 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: 0.9980 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.213698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.174557 restraints weight = 10382.556| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.73 r_work: 0.3832 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2050 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= 0.134 Angle : 0.546 7.908 13161 Z= 0.293 Chirality : 0.042 0.164 1493 Planarity : 0.004 0.053 1656 Dihedral : 4.542 28.625 1367 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.83 % Rotamer: Outliers : 3.74 % Allowed : 18.40 % Favored : 77.86 % 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: 0.59 (0.24), residues: 1200 helix: 1.76 (0.24), residues: 443 sheet: -0.09 (0.32), residues: 260 loop : -0.53 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 96 HIS 0.004 0.001 HIS A 209 PHE 0.015 0.001 PHE R 335 TYR 0.014 0.001 TYR R 191 ARG 0.007 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 1) link_NAG-ASN : angle 2.12469 ( 3) link_BETA1-4 : bond 0.00835 ( 1) link_BETA1-4 : angle 0.70283 ( 3) hydrogen bonds : bond 0.04641 ( 493) hydrogen bonds : angle 4.67812 ( 1374) SS BOND : bond 0.00177 ( 6) SS BOND : angle 0.73372 ( 12) covalent geometry : bond 0.00295 ( 9671) covalent geometry : angle 0.54486 (13143) Misc. bond : bond 0.00003 ( 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 181 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.063 Fit side-chains REVERT: R 32 MET cc_start: 0.6194 (mtp) cc_final: 0.5788 (ttm) REVERT: R 115 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7313 (mp) REVERT: A 17 LYS cc_start: 0.6647 (mttm) cc_final: 0.5953 (mtpt) REVERT: A 21 LYS cc_start: 0.6323 (tttm) cc_final: 0.5646 (mmpt) REVERT: A 43 ASN cc_start: 0.5379 (OUTLIER) cc_final: 0.4450 (t0) REVERT: A 73 LYS cc_start: 0.5856 (mttp) cc_final: 0.5447 (pttt) REVERT: A 126 LYS cc_start: 0.6281 (ttmt) cc_final: 0.5273 (pptt) REVERT: A 188 ARG cc_start: 0.5208 (ptm160) cc_final: 0.4989 (ptm160) REVERT: A 196 GLU cc_start: 0.4921 (mm-30) cc_final: 0.3936 (mm-30) REVERT: B 78 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8153 (tppt) REVERT: B 146 LEU cc_start: 0.8139 (mt) cc_final: 0.7914 (tp) REVERT: B 175 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: S 222 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6868 (mt-10) outliers start: 36 outliers final: 17 residues processed: 162 average time/residue: 1.1377 time to fit residues: 198.0618 Evaluate side-chains 153 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 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 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: 8.9990 chunk 116 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.212566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.173376 restraints weight = 10293.481| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 1.64 r_work: 0.3814 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9680 Z= 0.179 Angle : 0.587 7.916 13161 Z= 0.311 Chirality : 0.043 0.162 1493 Planarity : 0.004 0.052 1656 Dihedral : 4.596 25.678 1366 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 5.30 % Allowed : 16.32 % Favored : 78.38 % 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: 0.52 (0.24), residues: 1200 helix: 1.69 (0.24), residues: 446 sheet: -0.14 (0.32), residues: 260 loop : -0.57 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 112 HIS 0.006 0.001 HIS S 155 PHE 0.016 0.002 PHE R 335 TYR 0.039 0.002 TYR R 191 ARG 0.007 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 1) link_NAG-ASN : angle 1.96963 ( 3) link_BETA1-4 : bond 0.00764 ( 1) link_BETA1-4 : angle 0.78455 ( 3) hydrogen bonds : bond 0.04823 ( 493) hydrogen bonds : angle 4.72726 ( 1374) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.64825 ( 12) covalent geometry : bond 0.00414 ( 9671) covalent geometry : angle 0.58589 (13143) Misc. bond : bond 0.00013 ( 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 198 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 0.913 Fit side-chains REVERT: R 32 MET cc_start: 0.6155 (mtp) cc_final: 0.5820 (ttm) REVERT: R 115 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7360 (mp) REVERT: R 180 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6339 (mt-10) REVERT: A 10 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7457 (ttpt) REVERT: A 17 LYS cc_start: 0.6655 (mttm) cc_final: 0.5925 (mtpt) REVERT: A 21 LYS cc_start: 0.6354 (tttm) cc_final: 0.5663 (mmpt) REVERT: A 43 ASN cc_start: 0.5648 (OUTLIER) cc_final: 0.4358 (t0) REVERT: A 126 LYS cc_start: 0.6266 (ttmt) cc_final: 0.5222 (pptt) REVERT: A 196 GLU cc_start: 0.4942 (mm-30) cc_final: 0.3922 (mm-30) REVERT: B 78 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8126 (tppt) REVERT: B 146 LEU cc_start: 0.8223 (mt) cc_final: 0.7993 (tp) REVERT: B 252 LEU cc_start: 0.7461 (tt) cc_final: 0.7190 (tp) REVERT: S 67 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6624 (mtm180) REVERT: S 128 MET cc_start: 0.5608 (mpp) cc_final: 0.5350 (mpt) REVERT: S 192 SER cc_start: 0.7330 (t) cc_final: 0.7067 (m) REVERT: S 198 THR cc_start: 0.4367 (OUTLIER) cc_final: 0.3970 (p) REVERT: S 222 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6887 (mt-10) outliers start: 51 outliers final: 22 residues processed: 174 average time/residue: 1.0500 time to fit residues: 196.6416 Evaluate side-chains 168 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 189 MET Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 207 LEU 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 72 THR 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 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 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 67 ARG 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: 7.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.0570 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.0902 ------------------------------------------------------------------------------- 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 ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.214761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176187 restraints weight = 10373.469| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.63 r_work: 0.3832 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9680 Z= 0.127 Angle : 0.528 7.520 13161 Z= 0.282 Chirality : 0.041 0.159 1493 Planarity : 0.004 0.050 1656 Dihedral : 4.351 25.765 1366 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.00 % Favored : 97.92 % Rotamer: Outliers : 4.05 % Allowed : 18.81 % 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: 0.72 (0.25), residues: 1200 helix: 1.92 (0.24), residues: 447 sheet: -0.02 (0.32), residues: 258 loop : -0.54 (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 0.017 0.001 TYR R 191 ARG 0.007 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 2.07755 ( 3) link_BETA1-4 : bond 0.00911 ( 1) link_BETA1-4 : angle 0.76959 ( 3) hydrogen bonds : bond 0.04205 ( 493) hydrogen bonds : angle 4.49280 ( 1374) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.60851 ( 12) covalent geometry : bond 0.00282 ( 9671) covalent geometry : angle 0.52660 (13143) Misc. bond : bond 0.00008 ( 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 182 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.926 Fit side-chains REVERT: R 32 MET cc_start: 0.6086 (mtp) cc_final: 0.5691 (ttm) REVERT: R 115 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7367 (mp) REVERT: R 180 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6292 (mt-10) REVERT: A 17 LYS cc_start: 0.6609 (mttm) cc_final: 0.5885 (mtpt) REVERT: A 21 LYS cc_start: 0.6305 (tttm) cc_final: 0.5624 (mmpt) REVERT: A 43 ASN cc_start: 0.5700 (OUTLIER) cc_final: 0.4117 (t0) REVERT: A 126 LYS cc_start: 0.6291 (ttmt) cc_final: 0.5276 (pptt) REVERT: A 196 GLU cc_start: 0.4840 (mm-30) cc_final: 0.3864 (mm-30) REVERT: B 146 LEU cc_start: 0.8165 (mt) cc_final: 0.7961 (tp) REVERT: B 252 LEU cc_start: 0.7388 (tt) cc_final: 0.7120 (tp) REVERT: S 192 SER cc_start: 0.7344 (t) cc_final: 0.7095 (m) REVERT: S 198 THR cc_start: 0.4315 (OUTLIER) cc_final: 0.3917 (p) REVERT: S 222 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6835 (mt-10) outliers start: 39 outliers final: 18 residues processed: 159 average time/residue: 1.1381 time to fit residues: 194.3322 Evaluate side-chains 158 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 207 LEU 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 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 327 VAL Chi-restraints excluded: chain S residue 63 THR 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: 0.8980 chunk 90 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.212338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.173861 restraints weight = 10307.627| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.68 r_work: 0.3812 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9680 Z= 0.146 Angle : 0.545 7.335 13161 Z= 0.289 Chirality : 0.042 0.157 1493 Planarity : 0.004 0.049 1656 Dihedral : 4.366 25.950 1366 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Rotamer: Outliers : 4.05 % Allowed : 18.71 % Favored : 77.23 % 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: 0.74 (0.25), residues: 1200 helix: 1.97 (0.24), residues: 447 sheet: -0.06 (0.32), residues: 258 loop : -0.53 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.019 0.002 PHE B 241 TYR 0.016 0.001 TYR R 191 ARG 0.008 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 1) link_NAG-ASN : angle 1.99214 ( 3) link_BETA1-4 : bond 0.00666 ( 1) link_BETA1-4 : angle 0.82720 ( 3) hydrogen bonds : bond 0.04295 ( 493) hydrogen bonds : angle 4.48633 ( 1374) SS BOND : bond 0.00161 ( 6) SS BOND : angle 0.55295 ( 12) covalent geometry : bond 0.00333 ( 9671) covalent geometry : angle 0.54411 (13143) Misc. bond : bond 0.00013 ( 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 181 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.939 Fit side-chains REVERT: R 32 MET cc_start: 0.6096 (mtp) cc_final: 0.5814 (ttm) REVERT: R 115 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7390 (mp) REVERT: A 17 LYS cc_start: 0.6620 (mmtm) cc_final: 0.5942 (mtpt) REVERT: A 21 LYS cc_start: 0.6351 (tttm) cc_final: 0.5634 (mmpt) REVERT: A 126 LYS cc_start: 0.6301 (ttmt) cc_final: 0.5242 (pptt) REVERT: A 196 GLU cc_start: 0.4836 (mm-30) cc_final: 0.3822 (mm-30) REVERT: B 252 LEU cc_start: 0.7399 (tt) cc_final: 0.7133 (tp) REVERT: S 192 SER cc_start: 0.7308 (t) cc_final: 0.7056 (m) REVERT: S 198 THR cc_start: 0.4297 (OUTLIER) cc_final: 0.3911 (p) REVERT: S 222 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6875 (mt-10) outliers start: 39 outliers final: 24 residues processed: 157 average time/residue: 1.0880 time to fit residues: 184.2281 Evaluate side-chains 159 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain R residue 387 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 56 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 0.0020 chunk 100 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- 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 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.211024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.171887 restraints weight = 10343.567| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.64 r_work: 0.3809 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9680 Z= 0.179 Angle : 0.586 9.181 13161 Z= 0.308 Chirality : 0.043 0.161 1493 Planarity : 0.004 0.048 1656 Dihedral : 4.528 25.881 1366 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 4.26 % Allowed : 19.23 % Favored : 76.51 % 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: 0.69 (0.24), residues: 1200 helix: 1.87 (0.24), residues: 445 sheet: -0.17 (0.33), residues: 247 loop : -0.43 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.018 0.002 PHE R 335 TYR 0.033 0.002 TYR R 191 ARG 0.009 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 1) link_NAG-ASN : angle 1.89824 ( 3) link_BETA1-4 : bond 0.00789 ( 1) link_BETA1-4 : angle 0.84289 ( 3) hydrogen bonds : bond 0.04575 ( 493) hydrogen bonds : angle 4.61464 ( 1374) SS BOND : bond 0.00191 ( 6) SS BOND : angle 0.57756 ( 12) covalent geometry : bond 0.00415 ( 9671) covalent geometry : angle 0.58577 (13143) Misc. bond : bond 0.00019 ( 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 176 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.896 Fit side-chains REVERT: R 32 MET cc_start: 0.6026 (mtp) cc_final: 0.5807 (ttm) REVERT: R 115 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7381 (mp) REVERT: A 17 LYS cc_start: 0.6625 (mmtm) cc_final: 0.5892 (mtpt) REVERT: A 21 LYS cc_start: 0.6391 (tttm) cc_final: 0.5671 (mmpt) REVERT: A 22 ASN cc_start: 0.6831 (m-40) cc_final: 0.6563 (m-40) REVERT: A 126 LYS cc_start: 0.6300 (ttmt) cc_final: 0.5258 (pptt) REVERT: A 196 GLU cc_start: 0.4948 (mm-30) cc_final: 0.3918 (mm-30) REVERT: B 78 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8110 (ttmm) REVERT: B 252 LEU cc_start: 0.7435 (tt) cc_final: 0.7170 (tp) REVERT: S 67 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6675 (mtm180) REVERT: S 192 SER cc_start: 0.7319 (t) cc_final: 0.7062 (m) REVERT: S 198 THR cc_start: 0.4319 (OUTLIER) cc_final: 0.3908 (p) REVERT: S 222 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6884 (mt-10) outliers start: 41 outliers final: 29 residues processed: 155 average time/residue: 1.1168 time to fit residues: 186.3414 Evaluate side-chains 166 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 207 LEU 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 110 VAL Chi-restraints excluded: chain A residue 122 LEU 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 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 168 LEU 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 118 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS 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: 2.9990 chunk 40 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.214894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176630 restraints weight = 10511.078| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.66 r_work: 0.3848 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2834 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= 0.113 Angle : 0.513 7.079 13161 Z= 0.275 Chirality : 0.041 0.157 1493 Planarity : 0.004 0.046 1656 Dihedral : 4.221 26.042 1366 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.42 % Rotamer: Outliers : 3.95 % Allowed : 19.65 % 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: 2.11 (0.24), residues: 447 sheet: -0.05 (0.33), residues: 245 loop : -0.40 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.018 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 0.00217 ( 1) link_NAG-ASN : angle 2.01698 ( 3) link_BETA1-4 : bond 0.00691 ( 1) link_BETA1-4 : angle 0.85868 ( 3) hydrogen bonds : bond 0.03888 ( 493) hydrogen bonds : angle 4.33420 ( 1374) SS BOND : bond 0.00128 ( 6) SS BOND : angle 0.58457 ( 12) covalent geometry : bond 0.00248 ( 9671) covalent geometry : angle 0.51230 (13143) Misc. bond : bond 0.00009 ( 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 185 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.013 Fit side-chains REVERT: R 32 MET cc_start: 0.5946 (mtp) cc_final: 0.5745 (ttm) REVERT: R 115 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7450 (mp) REVERT: A 17 LYS cc_start: 0.6553 (mmtm) cc_final: 0.5848 (mtpt) REVERT: A 22 ASN cc_start: 0.6785 (m-40) cc_final: 0.6543 (m-40) REVERT: A 126 LYS cc_start: 0.6295 (ttmt) cc_final: 0.5265 (pptt) REVERT: A 196 GLU cc_start: 0.4809 (mm-30) cc_final: 0.3799 (mm-30) REVERT: B 252 LEU cc_start: 0.7313 (tt) cc_final: 0.7010 (tp) REVERT: S 67 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6756 (mtm180) REVERT: S 180 MET cc_start: 0.6027 (tpt) cc_final: 0.5669 (tpt) REVERT: S 198 THR cc_start: 0.4268 (OUTLIER) cc_final: 0.3844 (p) REVERT: S 222 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6853 (mt-10) outliers start: 38 outliers final: 26 residues processed: 163 average time/residue: 1.1352 time to fit residues: 199.2012 Evaluate side-chains 164 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain R residue 384 VAL 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 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 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 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: 0.6980 chunk 11 optimal weight: 0.0870 chunk 98 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 109 optimal weight: 0.0040 chunk 120 optimal weight: 5.9990 chunk 43 optimal weight: 0.0470 chunk 35 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 overall best weight: 0.3068 ------------------------------------------------------------------------------- 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 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.216998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.179423 restraints weight = 10424.956| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.62 r_work: 0.3877 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2978 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= 0.098 Angle : 0.518 9.489 13161 Z= 0.275 Chirality : 0.041 0.156 1493 Planarity : 0.004 0.046 1656 Dihedral : 4.092 26.214 1366 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.92 % Favored : 98.00 % Rotamer: Outliers : 3.22 % Allowed : 21.10 % Favored : 75.68 % 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: 1.02 (0.25), residues: 1200 helix: 2.23 (0.25), residues: 447 sheet: 0.07 (0.33), residues: 244 loop : -0.38 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.019 0.001 PHE R 453 TYR 0.018 0.001 TYR R 191 ARG 0.010 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 1) link_NAG-ASN : angle 2.00529 ( 3) link_BETA1-4 : bond 0.00738 ( 1) link_BETA1-4 : angle 0.91370 ( 3) hydrogen bonds : bond 0.03631 ( 493) hydrogen bonds : angle 4.24244 ( 1374) SS BOND : bond 0.00128 ( 6) SS BOND : angle 0.56266 ( 12) covalent geometry : bond 0.00204 ( 9671) covalent geometry : angle 0.51661 (13143) Misc. bond : bond 0.00003 ( 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 168 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: R 32 MET cc_start: 0.5821 (mtp) cc_final: 0.5609 (ttm) REVERT: R 115 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7435 (mp) REVERT: R 213 ARG cc_start: 0.7670 (mtp180) cc_final: 0.7192 (tpt90) REVERT: A 17 LYS cc_start: 0.6532 (mmtm) cc_final: 0.5825 (mtpt) REVERT: A 126 LYS cc_start: 0.6285 (ttmt) cc_final: 0.5279 (pptt) REVERT: A 196 GLU cc_start: 0.4690 (mm-30) cc_final: 0.3729 (mm-30) REVERT: B 252 LEU cc_start: 0.7264 (tt) cc_final: 0.6988 (tp) REVERT: S 83 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7084 (mtp) REVERT: S 180 MET cc_start: 0.5969 (tpt) cc_final: 0.5627 (tpt) REVERT: S 198 THR cc_start: 0.4150 (OUTLIER) cc_final: 0.3747 (p) outliers start: 31 outliers final: 21 residues processed: 152 average time/residue: 1.0820 time to fit residues: 177.0135 Evaluate side-chains 157 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 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 G residue 19 LEU 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 147 CYS 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: 2.9990 chunk 52 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.216270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.178560 restraints weight = 10495.842| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.65 r_work: 0.3868 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3056 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 : 0.523 7.374 13161 Z= 0.277 Chirality : 0.041 0.158 1493 Planarity : 0.004 0.046 1656 Dihedral : 4.096 26.218 1366 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 2.91 % Allowed : 21.31 % Favored : 75.78 % 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: 1.06 (0.25), residues: 1200 helix: 2.26 (0.25), residues: 447 sheet: 0.27 (0.32), residues: 248 loop : -0.46 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.020 0.001 PHE R 453 TYR 0.011 0.001 TYR R 443 ARG 0.011 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 1) link_NAG-ASN : angle 1.87486 ( 3) link_BETA1-4 : bond 0.00752 ( 1) link_BETA1-4 : angle 0.92808 ( 3) hydrogen bonds : bond 0.03730 ( 493) hydrogen bonds : angle 4.23739 ( 1374) SS BOND : bond 0.00138 ( 6) SS BOND : angle 0.98526 ( 12) covalent geometry : bond 0.00241 ( 9671) covalent geometry : angle 0.52153 (13143) Misc. bond : bond 0.00006 ( 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 163 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: R 115 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7480 (mp) REVERT: R 177 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5658 (pm20) REVERT: R 213 ARG cc_start: 0.7635 (mtp180) cc_final: 0.7152 (tpt90) REVERT: A 17 LYS cc_start: 0.6494 (mmtm) cc_final: 0.5771 (mtpt) REVERT: A 126 LYS cc_start: 0.6273 (ttmt) cc_final: 0.5265 (pptt) REVERT: A 196 GLU cc_start: 0.4668 (mm-30) cc_final: 0.3700 (mm-30) REVERT: B 252 LEU cc_start: 0.7330 (tt) cc_final: 0.7054 (tp) REVERT: S 38 ARG cc_start: 0.7964 (ptt180) cc_final: 0.7546 (pmm-80) REVERT: S 83 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7053 (mtp) REVERT: S 180 MET cc_start: 0.5952 (tpt) cc_final: 0.5630 (tpt) REVERT: S 198 THR cc_start: 0.4148 (OUTLIER) cc_final: 0.3751 (p) outliers start: 28 outliers final: 22 residues processed: 150 average time/residue: 1.1676 time to fit residues: 187.8755 Evaluate side-chains 157 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 327 VAL Chi-restraints excluded: chain G residue 19 LEU 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 147 CYS 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 88 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 102 optimal weight: 0.0670 chunk 68 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.0724 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.213405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175094 restraints weight = 10351.876| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.62 r_work: 0.3833 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9680 Z= 0.172 Angle : 0.585 9.330 13161 Z= 0.307 Chirality : 0.043 0.164 1493 Planarity : 0.004 0.046 1656 Dihedral : 4.292 26.281 1366 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Rotamer: Outliers : 2.91 % Allowed : 21.52 % Favored : 75.57 % 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: 0.94 (0.25), residues: 1200 helix: 2.13 (0.24), residues: 445 sheet: 0.08 (0.33), residues: 244 loop : -0.41 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 82 HIS 0.006 0.001 HIS G 44 PHE 0.022 0.002 PHE B 241 TYR 0.028 0.002 TYR R 191 ARG 0.010 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 1) link_NAG-ASN : angle 1.74889 ( 3) link_BETA1-4 : bond 0.00809 ( 1) link_BETA1-4 : angle 0.96916 ( 3) hydrogen bonds : bond 0.04255 ( 493) hydrogen bonds : angle 4.42386 ( 1374) SS BOND : bond 0.00218 ( 6) SS BOND : angle 0.97992 ( 12) covalent geometry : bond 0.00402 ( 9671) covalent geometry : angle 0.58361 (13143) Misc. bond : bond 0.00018 ( 1) =============================================================================== Job complete usr+sys time: 8382.07 seconds wall clock time: 145 minutes 42.26 seconds (8742.26 seconds total)