Starting phenix.real_space_refine on Thu Jan 16 12:32:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jr3_61747/01_2025/9jr3_61747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jr3_61747/01_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_61747/01_2025/9jr3_61747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jr3_61747/01_2025/9jr3_61747.map" model { file = "/net/cci-nas-00/data/ceres_data/9jr3_61747/01_2025/9jr3_61747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jr3_61747/01_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.66, per 1000 atoms: 0.70 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2302 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 39.4% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 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: 2.74 Time building geometry restraints manager: 2.84 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: 4.650 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: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.630 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.000 ------------------------------------------------------------------------------- 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 0.033 9671 Z= 0.174 Angle : 0.491 5.440 13143 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 *********************** 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 : 0.954 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: 1.1640 time to fit residues: 246.5456 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 : 0.964 ------------------------------------------------------------------------------- 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 9671 Z= 0.400 Angle : 0.670 8.028 13143 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 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.937 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: 1.1481 time to fit residues: 217.0877 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 : 0.964 ------------------------------------------------------------------------------- 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 9671 Z= 0.195 Angle : 0.545 7.908 13143 Z= 0.292 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 *********************** 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 : 0.998 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: 1.1960 time to fit residues: 208.2551 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 : 0.941 ------------------------------------------------------------------------------- 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: 2.9990 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: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4313 r_free = 0.4313 target = 0.212053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.172890 restraints weight = 10289.819| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.63 r_work: 0.3810 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9671 Z= 0.291 Angle : 0.600 7.776 13143 Z= 0.317 Chirality : 0.044 0.163 1493 Planarity : 0.004 0.053 1656 Dihedral : 4.663 25.667 1366 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.08 % Favored : 96.83 % Rotamer: Outliers : 5.30 % Allowed : 16.42 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1200 helix: 1.62 (0.24), residues: 446 sheet: -0.16 (0.32), residues: 260 loop : -0.58 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.007 0.001 HIS S 155 PHE 0.016 0.002 PHE R 335 TYR 0.027 0.002 TYR R 191 ARG 0.007 0.001 ARG A 208 *********************** 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 196 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 1.004 Fit side-chains REVERT: R 32 MET cc_start: 0.6167 (mtp) cc_final: 0.5833 (ttm) REVERT: R 115 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7383 (mp) REVERT: R 180 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6376 (mt-10) REVERT: A 17 LYS cc_start: 0.6656 (mttm) cc_final: 0.5932 (mtpt) REVERT: A 21 LYS cc_start: 0.6385 (tttm) cc_final: 0.5708 (mmpt) REVERT: A 43 ASN cc_start: 0.5688 (OUTLIER) cc_final: 0.4470 (t0) REVERT: A 126 LYS cc_start: 0.6307 (ttmt) cc_final: 0.5290 (pptt) REVERT: A 196 GLU cc_start: 0.5032 (mm-30) cc_final: 0.4002 (mm-30) REVERT: B 78 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8142 (tppt) REVERT: B 146 LEU cc_start: 0.8226 (mt) cc_final: 0.7999 (tp) REVERT: B 252 LEU cc_start: 0.7504 (tt) cc_final: 0.7232 (tp) REVERT: S 67 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6636 (mtm180) REVERT: S 128 MET cc_start: 0.5660 (mpp) cc_final: 0.5409 (mpt) REVERT: S 192 SER cc_start: 0.7366 (t) cc_final: 0.7105 (m) REVERT: S 198 THR cc_start: 0.4393 (OUTLIER) cc_final: 0.3995 (p) REVERT: S 222 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6864 (mt-10) outliers start: 51 outliers final: 22 residues processed: 173 average time/residue: 1.1710 time to fit residues: 217.6262 Evaluate side-chains 169 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.0270 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 overall best weight: 1.4442 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.211479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.172616 restraints weight = 10352.680| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.69 r_work: 0.3809 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9671 Z= 0.217 Angle : 0.546 7.585 13143 Z= 0.292 Chirality : 0.042 0.161 1493 Planarity : 0.004 0.051 1656 Dihedral : 4.475 25.702 1366 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.17 % Favored : 97.75 % Rotamer: Outliers : 4.47 % Allowed : 18.61 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1200 helix: 1.82 (0.24), residues: 447 sheet: -0.14 (0.32), residues: 260 loop : -0.55 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 96 HIS 0.004 0.001 HIS A 209 PHE 0.017 0.002 PHE R 453 TYR 0.018 0.001 TYR R 191 ARG 0.007 0.000 ARG A 208 *********************** 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 186 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.939 Fit side-chains REVERT: R 32 MET cc_start: 0.6117 (mtp) cc_final: 0.5737 (ttm) REVERT: R 115 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7385 (mp) REVERT: R 180 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6293 (mt-10) REVERT: A 17 LYS cc_start: 0.6599 (mttm) cc_final: 0.5875 (mtpt) REVERT: A 21 LYS cc_start: 0.6326 (tttm) cc_final: 0.5620 (mmpt) REVERT: A 43 ASN cc_start: 0.5652 (OUTLIER) cc_final: 0.4026 (t0) REVERT: A 126 LYS cc_start: 0.6282 (ttmt) cc_final: 0.5241 (pptt) REVERT: A 196 GLU cc_start: 0.4910 (mm-30) cc_final: 0.3895 (mm-30) REVERT: B 78 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8083 (tppt) REVERT: B 146 LEU cc_start: 0.8208 (mt) cc_final: 0.8007 (tp) REVERT: B 252 LEU cc_start: 0.7426 (tt) cc_final: 0.7148 (tp) REVERT: S 192 SER cc_start: 0.7326 (t) cc_final: 0.7065 (m) REVERT: S 198 THR cc_start: 0.4326 (OUTLIER) cc_final: 0.3930 (p) REVERT: S 222 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6892 (mt-10) outliers start: 43 outliers final: 22 residues processed: 160 average time/residue: 1.2226 time to fit residues: 210.1576 Evaluate side-chains 164 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 8 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.212706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.174330 restraints weight = 10331.654| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.69 r_work: 0.3834 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9671 Z= 0.178 Angle : 0.523 7.343 13143 Z= 0.279 Chirality : 0.041 0.158 1493 Planarity : 0.004 0.049 1656 Dihedral : 4.312 25.925 1366 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.50 % Rotamer: Outliers : 3.85 % Allowed : 19.54 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1200 helix: 2.02 (0.24), residues: 447 sheet: -0.02 (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 0.018 0.001 PHE B 241 TYR 0.014 0.001 TYR R 191 ARG 0.010 0.000 ARG A 208 *********************** 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 175 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.045 Fit side-chains REVERT: R 32 MET cc_start: 0.6060 (mtp) cc_final: 0.5779 (ttm) REVERT: R 115 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7386 (mp) REVERT: A 17 LYS cc_start: 0.6564 (mmtm) cc_final: 0.5868 (mtpt) REVERT: A 126 LYS cc_start: 0.6263 (ttmt) cc_final: 0.5225 (pptt) REVERT: A 196 GLU cc_start: 0.4782 (mm-30) cc_final: 0.3785 (mm-30) REVERT: B 146 LEU cc_start: 0.8183 (mt) cc_final: 0.7977 (tp) REVERT: B 252 LEU cc_start: 0.7345 (tt) cc_final: 0.7056 (tp) REVERT: S 180 MET cc_start: 0.6060 (tpt) cc_final: 0.5687 (tpt) REVERT: S 192 SER cc_start: 0.7288 (t) cc_final: 0.7032 (m) REVERT: S 198 THR cc_start: 0.4268 (OUTLIER) cc_final: 0.3862 (p) REVERT: S 222 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6852 (mt-10) outliers start: 37 outliers final: 23 residues processed: 154 average time/residue: 1.2129 time to fit residues: 200.5407 Evaluate side-chains 154 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 414 MET 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: 2.9990 chunk 14 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 6 optimal weight: 40.0000 chunk 34 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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** S 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.212004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.172942 restraints weight = 10358.021| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.66 r_work: 0.3811 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9671 Z= 0.239 Angle : 0.566 9.624 13143 Z= 0.298 Chirality : 0.042 0.157 1493 Planarity : 0.004 0.048 1656 Dihedral : 4.424 25.990 1366 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Rotamer: Outliers : 3.53 % Allowed : 19.75 % Favored : 76.72 % 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: 0.78 (0.24), residues: 1200 helix: 1.96 (0.24), residues: 445 sheet: -0.09 (0.33), residues: 245 loop : -0.42 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.017 0.002 PHE R 335 TYR 0.019 0.001 TYR R 191 ARG 0.009 0.000 ARG A 208 *********************** 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 170 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.984 Fit side-chains REVERT: R 32 MET cc_start: 0.6029 (mtp) cc_final: 0.5742 (ttm) REVERT: R 115 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7394 (mp) REVERT: A 17 LYS cc_start: 0.6598 (mmtm) cc_final: 0.5879 (mtpt) REVERT: A 22 ASN cc_start: 0.6806 (m-40) cc_final: 0.6523 (m-40) REVERT: A 126 LYS cc_start: 0.6276 (ttmt) cc_final: 0.5228 (pptt) REVERT: A 196 GLU cc_start: 0.4857 (mm-30) cc_final: 0.3840 (mm-30) REVERT: B 252 LEU cc_start: 0.7377 (tt) cc_final: 0.7104 (tp) REVERT: S 192 SER cc_start: 0.7300 (t) cc_final: 0.7042 (m) REVERT: S 198 THR cc_start: 0.4270 (OUTLIER) cc_final: 0.3872 (p) REVERT: S 222 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6860 (mt-10) outliers start: 34 outliers final: 27 residues processed: 151 average time/residue: 1.1715 time to fit residues: 190.3884 Evaluate side-chains 163 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU 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: 20.0000 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.213217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.174479 restraints weight = 10495.670| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.64 r_work: 0.3825 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9671 Z= 0.193 Angle : 0.528 7.265 13143 Z= 0.281 Chirality : 0.041 0.156 1493 Planarity : 0.004 0.046 1656 Dihedral : 4.300 25.983 1366 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 3.53 % Allowed : 20.06 % 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: 0.89 (0.25), residues: 1200 helix: 2.06 (0.24), residues: 447 sheet: 0.07 (0.32), residues: 256 loop : -0.45 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.019 0.001 PHE B 241 TYR 0.013 0.001 TYR R 191 ARG 0.010 0.000 ARG A 208 *********************** 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 173 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.033 Fit side-chains REVERT: R 32 MET cc_start: 0.5972 (mtp) cc_final: 0.5767 (ttm) REVERT: R 115 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7433 (mp) REVERT: A 17 LYS cc_start: 0.6596 (mmtm) cc_final: 0.5892 (mtpt) REVERT: A 22 ASN cc_start: 0.6804 (m-40) cc_final: 0.6545 (m-40) REVERT: A 126 LYS cc_start: 0.6296 (ttmt) cc_final: 0.5246 (pptt) REVERT: A 196 GLU cc_start: 0.4839 (mm-30) cc_final: 0.3817 (mm-30) REVERT: B 252 LEU cc_start: 0.7332 (tt) cc_final: 0.7056 (tp) REVERT: S 67 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6747 (mtm180) REVERT: S 128 MET cc_start: 0.6048 (mpp) cc_final: 0.5792 (mpt) REVERT: S 180 MET cc_start: 0.6039 (tpt) cc_final: 0.5675 (tpt) REVERT: S 192 SER cc_start: 0.7286 (t) cc_final: 0.7074 (m) REVERT: S 198 THR cc_start: 0.4225 (OUTLIER) cc_final: 0.3810 (p) REVERT: S 222 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6835 (mt-10) outliers start: 34 outliers final: 24 residues processed: 154 average time/residue: 1.2330 time to fit residues: 203.6951 Evaluate side-chains 157 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 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 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 181 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 22 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4340 r_free = 0.4340 target = 0.215233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177235 restraints weight = 10361.287| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.64 r_work: 0.3853 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9671 Z= 0.158 Angle : 0.527 9.424 13143 Z= 0.279 Chirality : 0.041 0.156 1493 Planarity : 0.004 0.046 1656 Dihedral : 4.185 25.965 1366 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 3.53 % Allowed : 20.58 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1200 helix: 2.13 (0.24), residues: 447 sheet: -0.04 (0.33), residues: 245 loop : -0.37 (0.28), residues: 508 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 B 241 TYR 0.031 0.001 TYR R 191 ARG 0.010 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.990 Fit side-chains REVERT: R 32 MET cc_start: 0.5912 (mtp) cc_final: 0.5706 (ttm) REVERT: R 115 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7442 (mp) REVERT: A 17 LYS cc_start: 0.6531 (mmtm) cc_final: 0.5819 (mtpt) REVERT: A 126 LYS cc_start: 0.6264 (ttmt) cc_final: 0.5254 (pptt) REVERT: A 196 GLU cc_start: 0.4769 (mm-30) cc_final: 0.3765 (mm-30) REVERT: B 252 LEU cc_start: 0.7321 (tt) cc_final: 0.7045 (tp) REVERT: S 67 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6699 (mtm180) REVERT: S 83 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.7068 (mtp) REVERT: S 180 MET cc_start: 0.5966 (tpt) cc_final: 0.5611 (tpt) REVERT: S 198 THR cc_start: 0.4192 (OUTLIER) cc_final: 0.3784 (p) REVERT: S 222 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6831 (mt-10) outliers start: 34 outliers final: 23 residues processed: 153 average time/residue: 1.2297 time to fit residues: 203.0378 Evaluate side-chains 159 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 414 MET 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 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG 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: 4.9990 chunk 52 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.215014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176959 restraints weight = 10442.454| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.62 r_work: 0.3850 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9671 Z= 0.173 Angle : 0.525 7.208 13143 Z= 0.280 Chirality : 0.041 0.154 1493 Planarity : 0.004 0.045 1656 Dihedral : 4.149 26.140 1366 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 3.22 % Allowed : 20.89 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1200 helix: 2.16 (0.24), residues: 447 sheet: -0.02 (0.33), residues: 245 loop : -0.38 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 82 HIS 0.006 0.001 HIS G 44 PHE 0.020 0.001 PHE R 453 TYR 0.016 0.001 TYR R 191 ARG 0.011 0.000 ARG A 208 ********************** 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 166 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.993 Fit side-chains REVERT: R 32 MET cc_start: 0.5894 (mtp) cc_final: 0.5669 (ttm) REVERT: R 115 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7468 (mp) REVERT: R 213 ARG cc_start: 0.7721 (mtp180) cc_final: 0.7240 (tpt90) REVERT: A 17 LYS cc_start: 0.6531 (mmtm) cc_final: 0.5816 (mtpt) REVERT: A 126 LYS cc_start: 0.6291 (ttmt) cc_final: 0.5287 (pptt) REVERT: A 196 GLU cc_start: 0.4816 (mm-30) cc_final: 0.3812 (mm-30) REVERT: B 252 LEU cc_start: 0.7333 (tt) cc_final: 0.7068 (tp) REVERT: S 67 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6714 (mtm180) REVERT: S 83 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7073 (mtp) REVERT: S 180 MET cc_start: 0.5988 (tpt) cc_final: 0.5676 (tpt) REVERT: S 198 THR cc_start: 0.4190 (OUTLIER) cc_final: 0.3805 (p) REVERT: S 222 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6857 (mt-10) outliers start: 31 outliers final: 22 residues processed: 150 average time/residue: 1.2957 time to fit residues: 208.7539 Evaluate side-chains 157 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 R residue 414 MET Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 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 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG 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: 0.8980 chunk 44 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 29 optimal weight: 0.0070 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 30.0000 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 overall best weight: 1.4202 ------------------------------------------------------------------------------- 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** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.213879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.175896 restraints weight = 10315.212| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.60 r_work: 0.3833 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9671 Z= 0.207 Angle : 0.561 10.516 13143 Z= 0.295 Chirality : 0.042 0.157 1493 Planarity : 0.004 0.046 1656 Dihedral : 4.232 26.047 1366 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 3.85 % Allowed : 20.89 % Favored : 75.26 % 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: 0.91 (0.25), residues: 1200 helix: 2.12 (0.24), residues: 445 sheet: -0.02 (0.33), residues: 247 loop : -0.38 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 82 HIS 0.006 0.001 HIS G 44 PHE 0.023 0.002 PHE R 453 TYR 0.013 0.001 TYR R 191 ARG 0.010 0.000 ARG A 208 =============================================================================== Job complete usr+sys time: 8633.34 seconds wall clock time: 153 minutes 39.82 seconds (9219.82 seconds total)