Starting phenix.real_space_refine on Wed Jan 15 22:52:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn2_39412/01_2025/8yn2_39412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn2_39412/01_2025/8yn2_39412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yn2_39412/01_2025/8yn2_39412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn2_39412/01_2025/8yn2_39412.map" model { file = "/net/cci-nas-00/data/ceres_data/8yn2_39412/01_2025/8yn2_39412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn2_39412/01_2025/8yn2_39412.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 5763 2.51 5 N 1531 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1798 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2196 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 148 Unusual residues: {'CLR': 5, 'HSM': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.39, per 1000 atoms: 0.60 Number of scatterers: 8979 At special positions: 0 Unit cell: (97.37, 107, 117.7, 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 1625 8.00 N 1531 7.00 C 5763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS R 441 " - pdb=" SG CYS R 444 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.0 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 40.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.557A pdb=" N ARG A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.663A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 4.152A 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: 4.318A 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 removed outlier: 3.586A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 356 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.509A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.526A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 55 removed outlier: 3.570A pdb=" N ARG R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 79 removed outlier: 4.188A pdb=" N TYR R 65 " --> pdb=" O VAL R 61 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE R 66 " --> pdb=" O GLY R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 removed outlier: 3.562A pdb=" N MET R 83 " --> pdb=" O VAL R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 131 Processing helix chain 'R' and resid 131 through 138 removed outlier: 3.544A pdb=" N LEU R 136 " --> pdb=" O PRO R 132 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS R 137 " --> pdb=" O LEU R 133 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR R 138 " --> pdb=" O ARG R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 156 Processing helix chain 'R' and resid 158 through 164 Processing helix chain 'R' and resid 164 through 169 Processing helix chain 'R' and resid 182 through 186 removed outlier: 4.446A pdb=" N ASP R 186 " --> pdb=" O ASP R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 199 removed outlier: 3.863A pdb=" N LYS R 191 " --> pdb=" O VAL R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 225 Processing helix chain 'R' and resid 410 through 442 removed outlier: 3.542A pdb=" N PHE R 424 " --> pdb=" O ILE R 420 " (cutoff:3.500A) Proline residue: R 430 - end of helix removed outlier: 3.681A pdb=" N MET R 436 " --> pdb=" O PHE R 432 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA R 439 " --> pdb=" O PHE R 435 " (cutoff:3.500A) Processing helix chain 'R' and resid 446 through 472 removed outlier: 3.805A pdb=" N SER R 461 " --> pdb=" O GLY R 457 " (cutoff:3.500A) Proline residue: R 465 - end of helix Proline residue: R 469 - end of helix removed outlier: 3.731A pdb=" N ASN R 472 " --> pdb=" O TYR R 468 " (cutoff:3.500A) Processing helix chain 'R' and resid 472 through 485 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 6.177A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL A 86 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N LEU A 38 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.626A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.751A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.963A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.296A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.384A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.514A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.738A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.794A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.305A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.106A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1299 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: 2.65 Time building geometry restraints manager: 2.75 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: 2869 1.34 - 1.46: 2246 1.46 - 1.58: 3985 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 9187 Sorted by residual: bond pdb=" CG HSM R 701 " pdb=" ND1 HSM R 701 " ideal model delta sigma weight residual 1.383 1.338 0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" C5 CLR R 706 " pdb=" C6 CLR R 706 " ideal model delta sigma weight residual 1.332 1.297 0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" C5 CLR R 703 " pdb=" C6 CLR R 703 " ideal model delta sigma weight residual 1.332 1.299 0.033 2.00e-02 2.50e+03 2.80e+00 bond pdb=" C5 CLR R 704 " pdb=" C6 CLR R 704 " ideal model delta sigma weight residual 1.332 1.299 0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C5 CLR R 705 " pdb=" C6 CLR R 705 " ideal model delta sigma weight residual 1.332 1.299 0.033 2.00e-02 2.50e+03 2.72e+00 ... (remaining 9182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12249 1.64 - 3.29: 174 3.29 - 4.93: 38 4.93 - 6.57: 21 6.57 - 8.21: 4 Bond angle restraints: 12486 Sorted by residual: angle pdb=" C13 CLR R 704 " pdb=" C17 CLR R 704 " pdb=" C20 CLR R 704 " ideal model delta sigma weight residual 119.60 111.39 8.21 3.00e+00 1.11e-01 7.50e+00 angle pdb=" C13 CLR R 702 " pdb=" C17 CLR R 702 " pdb=" C20 CLR R 702 " ideal model delta sigma weight residual 119.60 111.42 8.18 3.00e+00 1.11e-01 7.44e+00 angle pdb=" C13 CLR R 705 " pdb=" C17 CLR R 705 " pdb=" C20 CLR R 705 " ideal model delta sigma weight residual 119.60 111.60 8.00 3.00e+00 1.11e-01 7.12e+00 angle pdb=" C13 CLR R 703 " pdb=" C17 CLR R 703 " pdb=" C20 CLR R 703 " ideal model delta sigma weight residual 119.60 111.75 7.85 3.00e+00 1.11e-01 6.84e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.94 -4.40 1.91e+00 2.74e-01 5.30e+00 ... (remaining 12481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 5346 15.12 - 30.24: 241 30.24 - 45.36: 65 45.36 - 60.48: 17 60.48 - 75.60: 2 Dihedral angle restraints: 5671 sinusoidal: 2384 harmonic: 3287 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1329 0.099 - 0.198: 75 0.198 - 0.297: 5 0.297 - 0.395: 5 0.395 - 0.494: 5 Chirality restraints: 1419 Sorted by residual: chirality pdb=" C14 CLR R 704 " pdb=" C13 CLR R 704 " pdb=" C15 CLR R 704 " pdb=" C8 CLR R 704 " both_signs ideal model delta sigma weight residual False -2.32 -2.81 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" C14 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C15 CLR R 702 " pdb=" C8 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C14 CLR R 705 " pdb=" C13 CLR R 705 " pdb=" C15 CLR R 705 " pdb=" C8 CLR R 705 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.55e+00 ... (remaining 1416 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO B 194 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 184 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.79e-01 pdb=" N PRO E 185 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO E 185 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 185 " -0.014 5.00e-02 4.00e+02 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 317 2.72 - 3.27: 8894 3.27 - 3.81: 14811 3.81 - 4.36: 19092 4.36 - 4.90: 32503 Nonbonded interactions: 75617 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.180 3.040 nonbonded pdb=" OG1 THR R 41 " pdb=" OG1 THR R 462 " model vdw 2.270 3.040 nonbonded pdb=" O THR R 41 " pdb=" ND2 ASN R 45 " model vdw 2.288 3.120 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.289 3.120 nonbonded pdb=" NE2 GLN A 52 " pdb=" O ALA A 218 " model vdw 2.303 3.120 ... (remaining 75612 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: 0.510 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.460 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 0.045 9187 Z= 0.197 Angle : 0.559 8.214 12486 Z= 0.251 Chirality : 0.058 0.494 1419 Planarity : 0.003 0.043 1551 Dihedral : 9.777 75.596 3537 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.64 % Allowed : 2.97 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1113 helix: 1.30 (0.25), residues: 401 sheet: 0.81 (0.30), residues: 285 loop : 0.66 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE B 151 TYR 0.011 0.001 TYR E 190 ARG 0.002 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 210 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8554 (mttt) cc_final: 0.8242 (mtmt) REVERT: A 21 LYS cc_start: 0.8540 (tttm) cc_final: 0.8055 (mtmm) REVERT: A 73 LYS cc_start: 0.8531 (mttt) cc_final: 0.8315 (mptt) REVERT: A 208 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7274 (mtm180) REVERT: A 346 ASP cc_start: 0.8003 (m-30) cc_final: 0.7570 (t0) REVERT: B 16 ASN cc_start: 0.7831 (m-40) cc_final: 0.7597 (m110) REVERT: B 130 GLU cc_start: 0.8422 (mp0) cc_final: 0.8185 (mp0) REVERT: B 134 ARG cc_start: 0.8369 (ptt180) cc_final: 0.8115 (ptp90) REVERT: B 135 VAL cc_start: 0.9322 (t) cc_final: 0.9080 (p) REVERT: B 186 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8378 (m-30) REVERT: B 188 MET cc_start: 0.8971 (mmm) cc_final: 0.8685 (mmm) REVERT: C 20 LYS cc_start: 0.8683 (mttt) cc_final: 0.8346 (mttm) REVERT: E 43 LYS cc_start: 0.8100 (mmtm) cc_final: 0.7648 (mtpt) REVERT: R 55 GLU cc_start: 0.7388 (tp30) cc_final: 0.6897 (tp30) REVERT: R 57 LYS cc_start: 0.8056 (mttt) cc_final: 0.7438 (pttp) REVERT: R 176 ARG cc_start: 0.7487 (ptp90) cc_final: 0.7186 (ptp90) REVERT: R 179 LYS cc_start: 0.7501 (mmtt) cc_final: 0.6869 (mmmm) REVERT: R 215 LYS cc_start: 0.7502 (tppt) cc_final: 0.7287 (mppt) REVERT: R 218 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7736 (ttp-170) REVERT: R 470 LEU cc_start: 0.7968 (tt) cc_final: 0.7440 (mm) outliers start: 6 outliers final: 3 residues processed: 213 average time/residue: 1.4609 time to fit residues: 328.9008 Evaluate side-chains 156 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 441 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 116 ASN A 350 GLN B 91 HIS B 176 GLN B 220 GLN R 166 ASN R 472 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109726 restraints weight = 10841.637| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.97 r_work: 0.3110 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9187 Z= 0.167 Angle : 0.526 6.090 12486 Z= 0.282 Chirality : 0.043 0.183 1419 Planarity : 0.004 0.043 1551 Dihedral : 6.115 57.068 1568 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.02 % Allowed : 9.77 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.25), residues: 1113 helix: 2.41 (0.25), residues: 394 sheet: 1.00 (0.30), residues: 270 loop : 0.48 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.014 0.001 PHE A 74 TYR 0.020 0.001 TYR E 190 ARG 0.008 0.001 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8515 (mttt) cc_final: 0.8141 (mtmt) REVERT: A 82 HIS cc_start: 0.8231 (t-90) cc_final: 0.7870 (t-170) REVERT: A 208 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7329 (mtm180) REVERT: B 130 GLU cc_start: 0.8470 (mp0) cc_final: 0.8003 (mp0) REVERT: B 134 ARG cc_start: 0.8649 (ptt180) cc_final: 0.8400 (ptt-90) REVERT: B 188 MET cc_start: 0.8946 (mmm) cc_final: 0.8578 (mmm) REVERT: E 43 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7692 (mtpt) REVERT: E 213 THR cc_start: 0.8619 (p) cc_final: 0.8155 (t) REVERT: R 55 GLU cc_start: 0.7154 (tp30) cc_final: 0.6947 (tp30) REVERT: R 57 LYS cc_start: 0.8035 (mttt) cc_final: 0.7615 (mtmm) REVERT: R 470 LEU cc_start: 0.7902 (tt) cc_final: 0.7475 (mm) outliers start: 19 outliers final: 7 residues processed: 161 average time/residue: 1.2604 time to fit residues: 216.1575 Evaluate side-chains 153 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 441 CYS Chi-restraints excluded: chain R residue 454 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 79 optimal weight: 0.0970 chunk 37 optimal weight: 0.5980 chunk 94 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 13 GLN B 16 ASN E 171 ASN E 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104407 restraints weight = 10468.958| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.10 r_work: 0.3029 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9187 Z= 0.130 Angle : 0.476 5.884 12486 Z= 0.253 Chirality : 0.041 0.142 1419 Planarity : 0.004 0.042 1551 Dihedral : 5.710 56.611 1564 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.34 % Allowed : 12.42 % Favored : 85.24 % 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: 2.13 (0.25), residues: 1113 helix: 2.86 (0.25), residues: 391 sheet: 0.91 (0.30), residues: 268 loop : 0.53 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 82 PHE 0.018 0.001 PHE R 434 TYR 0.018 0.001 TYR E 190 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8327 (mttt) cc_final: 0.7935 (mtmt) REVERT: A 82 HIS cc_start: 0.8132 (t-90) cc_final: 0.7725 (t-170) REVERT: A 208 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7264 (mtm180) REVERT: B 130 GLU cc_start: 0.8456 (mp0) cc_final: 0.8152 (mp0) REVERT: B 258 ASP cc_start: 0.8778 (t70) cc_final: 0.8516 (t0) REVERT: E 43 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7473 (mtpt) REVERT: E 76 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8396 (mmtm) REVERT: E 213 THR cc_start: 0.8537 (p) cc_final: 0.8066 (t) REVERT: E 217 SER cc_start: 0.8256 (m) cc_final: 0.7851 (p) REVERT: R 57 LYS cc_start: 0.7864 (mttt) cc_final: 0.7430 (mtmm) REVERT: R 470 LEU cc_start: 0.7815 (tt) cc_final: 0.7368 (mm) outliers start: 22 outliers final: 10 residues processed: 163 average time/residue: 1.2847 time to fit residues: 223.3445 Evaluate side-chains 147 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain R residue 441 CYS Chi-restraints excluded: chain R residue 454 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 0.2980 chunk 90 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102600 restraints weight = 10375.175| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.11 r_work: 0.3002 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9187 Z= 0.160 Angle : 0.485 5.988 12486 Z= 0.257 Chirality : 0.041 0.138 1419 Planarity : 0.003 0.043 1551 Dihedral : 5.657 56.933 1564 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.44 % Allowed : 14.12 % Favored : 83.44 % 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: 2.13 (0.26), residues: 1113 helix: 3.01 (0.25), residues: 390 sheet: 0.72 (0.31), residues: 268 loop : 0.52 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 82 PHE 0.012 0.001 PHE A 74 TYR 0.015 0.001 TYR E 190 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8321 (mttt) cc_final: 0.7922 (mtmt) REVERT: A 82 HIS cc_start: 0.8049 (OUTLIER) cc_final: 0.7644 (t-170) REVERT: A 208 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7298 (mtm180) REVERT: A 217 CYS cc_start: 0.8269 (m) cc_final: 0.7842 (t) REVERT: B 130 GLU cc_start: 0.8620 (mp0) cc_final: 0.8394 (mp0) REVERT: B 258 ASP cc_start: 0.8782 (t70) cc_final: 0.8498 (t0) REVERT: E 43 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7483 (mtpt) REVERT: E 213 THR cc_start: 0.8570 (p) cc_final: 0.8132 (t) REVERT: E 217 SER cc_start: 0.8196 (m) cc_final: 0.7789 (p) REVERT: R 55 GLU cc_start: 0.7063 (tp30) cc_final: 0.6808 (tp30) REVERT: R 57 LYS cc_start: 0.7966 (mttt) cc_final: 0.7320 (pttp) REVERT: R 470 LEU cc_start: 0.7798 (tt) cc_final: 0.7302 (mm) outliers start: 23 outliers final: 12 residues processed: 155 average time/residue: 1.2696 time to fit residues: 210.0489 Evaluate side-chains 146 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 441 CYS Chi-restraints excluded: chain R residue 454 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 43 optimal weight: 0.0770 chunk 97 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108925 restraints weight = 10855.717| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.00 r_work: 0.3091 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9187 Z= 0.176 Angle : 0.489 6.241 12486 Z= 0.258 Chirality : 0.041 0.145 1419 Planarity : 0.003 0.043 1551 Dihedral : 5.621 56.342 1564 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.65 % Allowed : 14.44 % Favored : 82.91 % 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: 2.12 (0.26), residues: 1113 helix: 3.01 (0.25), residues: 391 sheet: 0.68 (0.31), residues: 268 loop : 0.51 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS A 82 PHE 0.013 0.001 PHE R 434 TYR 0.014 0.001 TYR E 190 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8444 (mttt) cc_final: 0.8068 (mtmt) REVERT: A 82 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7741 (t-170) REVERT: A 208 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7372 (mtm180) REVERT: A 217 CYS cc_start: 0.8282 (m) cc_final: 0.7986 (t) REVERT: B 258 ASP cc_start: 0.8831 (t70) cc_final: 0.8586 (t0) REVERT: E 43 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7702 (mtpt) REVERT: E 213 THR cc_start: 0.8662 (p) cc_final: 0.8241 (t) REVERT: E 217 SER cc_start: 0.8303 (m) cc_final: 0.7915 (p) REVERT: R 57 LYS cc_start: 0.8002 (mttt) cc_final: 0.7419 (pttp) REVERT: R 470 LEU cc_start: 0.7950 (tt) cc_final: 0.7492 (mm) outliers start: 25 outliers final: 15 residues processed: 151 average time/residue: 1.2828 time to fit residues: 206.8483 Evaluate side-chains 144 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP 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 209 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 441 CYS Chi-restraints excluded: chain R residue 454 ILE Chi-restraints excluded: chain R residue 483 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 16 ASN R 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109565 restraints weight = 10770.562| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.00 r_work: 0.3100 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9187 Z= 0.157 Angle : 0.482 6.794 12486 Z= 0.254 Chirality : 0.041 0.139 1419 Planarity : 0.003 0.042 1551 Dihedral : 5.529 56.333 1564 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.76 % Allowed : 15.29 % Favored : 81.95 % 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: 2.17 (0.26), residues: 1113 helix: 3.09 (0.25), residues: 391 sheet: 0.64 (0.31), residues: 273 loop : 0.55 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 82 PHE 0.011 0.001 PHE A 74 TYR 0.015 0.001 TYR E 190 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8446 (mttt) cc_final: 0.8065 (mtmt) REVERT: A 31 ARG cc_start: 0.8293 (mtt90) cc_final: 0.8072 (mtt90) REVERT: A 82 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7791 (t-170) REVERT: A 208 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7372 (mtm180) REVERT: A 217 CYS cc_start: 0.8336 (m) cc_final: 0.8038 (t) REVERT: B 130 GLU cc_start: 0.8591 (mp0) cc_final: 0.8243 (mp0) REVERT: B 258 ASP cc_start: 0.8796 (t70) cc_final: 0.8543 (t0) REVERT: E 43 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7695 (mtpt) REVERT: E 213 THR cc_start: 0.8650 (p) cc_final: 0.8242 (t) REVERT: E 217 SER cc_start: 0.8316 (m) cc_final: 0.7937 (p) REVERT: R 57 LYS cc_start: 0.7985 (mttt) cc_final: 0.7603 (mtmm) REVERT: R 470 LEU cc_start: 0.7946 (tt) cc_final: 0.7478 (mm) outliers start: 26 outliers final: 17 residues processed: 153 average time/residue: 1.3136 time to fit residues: 214.2072 Evaluate side-chains 152 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP 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 209 HIS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 441 CYS Chi-restraints excluded: chain R residue 454 ILE Chi-restraints excluded: chain R residue 483 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN R 198 ASN R 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.107041 restraints weight = 10947.855| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.01 r_work: 0.3058 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9187 Z= 0.233 Angle : 0.522 8.328 12486 Z= 0.274 Chirality : 0.042 0.159 1419 Planarity : 0.004 0.041 1551 Dihedral : 5.661 54.848 1564 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.55 % Allowed : 15.18 % Favored : 82.27 % 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: 2.08 (0.25), residues: 1113 helix: 2.98 (0.25), residues: 391 sheet: 0.66 (0.31), residues: 253 loop : 0.48 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.005 0.001 HIS A 82 PHE 0.012 0.001 PHE R 435 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8473 (mttt) cc_final: 0.8095 (mtmt) REVERT: A 82 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7772 (t-170) REVERT: A 208 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7383 (mtm180) REVERT: A 217 CYS cc_start: 0.8307 (m) cc_final: 0.8013 (t) REVERT: B 219 ARG cc_start: 0.8507 (mtt-85) cc_final: 0.8271 (mtt-85) REVERT: B 258 ASP cc_start: 0.8858 (t70) cc_final: 0.8597 (t0) REVERT: E 43 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7908 (mmpt) REVERT: E 174 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8776 (tt) REVERT: E 213 THR cc_start: 0.8651 (p) cc_final: 0.8255 (t) REVERT: R 57 LYS cc_start: 0.8039 (mttt) cc_final: 0.7461 (pttp) REVERT: R 176 ARG cc_start: 0.7508 (ptp90) cc_final: 0.7295 (ptp-170) REVERT: R 436 MET cc_start: 0.8599 (mtm) cc_final: 0.8345 (mtm) REVERT: R 470 LEU cc_start: 0.8092 (tt) cc_final: 0.7524 (mm) outliers start: 24 outliers final: 17 residues processed: 150 average time/residue: 1.3866 time to fit residues: 221.0479 Evaluate side-chains 151 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP 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 209 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 441 CYS Chi-restraints excluded: chain R residue 454 ILE Chi-restraints excluded: chain R residue 482 ILE Chi-restraints excluded: chain R residue 483 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 75 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 16 ASN R 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.147623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109867 restraints weight = 11062.790| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.02 r_work: 0.3099 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9187 Z= 0.140 Angle : 0.486 7.657 12486 Z= 0.255 Chirality : 0.040 0.151 1419 Planarity : 0.003 0.040 1551 Dihedral : 5.478 55.877 1564 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.02 % Allowed : 15.92 % Favored : 82.06 % 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: 2.12 (0.26), residues: 1113 helix: 3.11 (0.25), residues: 391 sheet: 0.50 (0.31), residues: 270 loop : 0.55 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 82 PHE 0.012 0.001 PHE R 434 TYR 0.018 0.001 TYR E 190 ARG 0.014 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8442 (mttt) cc_final: 0.8056 (mtmt) REVERT: A 82 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7685 (t-170) REVERT: A 208 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7352 (mtm180) REVERT: A 217 CYS cc_start: 0.8248 (m) cc_final: 0.7997 (t) REVERT: B 130 GLU cc_start: 0.8606 (mp0) cc_final: 0.8287 (mp0) REVERT: B 219 ARG cc_start: 0.8542 (mtt-85) cc_final: 0.8259 (mtt-85) REVERT: B 258 ASP cc_start: 0.8784 (t70) cc_final: 0.8520 (t0) REVERT: B 327 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8868 (p) REVERT: E 43 LYS cc_start: 0.8198 (mmtm) cc_final: 0.7677 (mtpt) REVERT: E 174 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8771 (tt) REVERT: E 213 THR cc_start: 0.8641 (p) cc_final: 0.8258 (t) REVERT: R 55 GLU cc_start: 0.7250 (tp30) cc_final: 0.7023 (tp30) REVERT: R 57 LYS cc_start: 0.7839 (mttt) cc_final: 0.7257 (pttp) REVERT: R 470 LEU cc_start: 0.8118 (tt) cc_final: 0.7887 (tp) outliers start: 19 outliers final: 11 residues processed: 149 average time/residue: 1.3010 time to fit residues: 206.3749 Evaluate side-chains 147 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 209 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain R residue 441 CYS Chi-restraints excluded: chain R residue 454 ILE Chi-restraints excluded: chain R residue 483 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN R 472 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107547 restraints weight = 10913.429| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.01 r_work: 0.3087 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9187 Z= 0.212 Angle : 0.514 8.923 12486 Z= 0.269 Chirality : 0.042 0.160 1419 Planarity : 0.004 0.042 1551 Dihedral : 5.603 55.175 1564 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.23 % Allowed : 15.92 % Favored : 81.85 % 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: 2.06 (0.25), residues: 1113 helix: 3.05 (0.25), residues: 391 sheet: 0.52 (0.30), residues: 269 loop : 0.48 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.005 0.001 HIS A 82 PHE 0.013 0.001 PHE R 434 TYR 0.013 0.001 TYR E 190 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8483 (mttt) cc_final: 0.8103 (mtmt) REVERT: A 82 HIS cc_start: 0.8050 (OUTLIER) cc_final: 0.7727 (t-170) REVERT: A 208 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7418 (mtm180) REVERT: A 217 CYS cc_start: 0.8235 (m) cc_final: 0.8009 (t) REVERT: B 13 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7642 (tp-100) REVERT: B 130 GLU cc_start: 0.8687 (mp0) cc_final: 0.8466 (mp0) REVERT: B 197 ARG cc_start: 0.8370 (mpt90) cc_final: 0.8166 (mpt90) REVERT: B 219 ARG cc_start: 0.8501 (mtt-85) cc_final: 0.8287 (mmt90) REVERT: B 258 ASP cc_start: 0.8851 (t70) cc_final: 0.8615 (t0) REVERT: E 43 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7907 (mmpt) REVERT: E 174 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8795 (tt) REVERT: E 213 THR cc_start: 0.8645 (p) cc_final: 0.8256 (t) REVERT: R 57 LYS cc_start: 0.8018 (mttt) cc_final: 0.7440 (pttp) REVERT: R 436 MET cc_start: 0.8639 (mtm) cc_final: 0.8376 (mtm) REVERT: R 470 LEU cc_start: 0.8165 (tt) cc_final: 0.7921 (tp) outliers start: 21 outliers final: 14 residues processed: 145 average time/residue: 1.3170 time to fit residues: 204.5886 Evaluate side-chains 147 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 209 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 441 CYS Chi-restraints excluded: chain R residue 454 ILE Chi-restraints excluded: chain R residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 13 GLN R 416 GLN R 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.147780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.109966 restraints weight = 10982.433| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.02 r_work: 0.3126 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9187 Z= 0.142 Angle : 0.488 8.866 12486 Z= 0.253 Chirality : 0.041 0.156 1419 Planarity : 0.003 0.041 1551 Dihedral : 5.445 56.213 1564 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.59 % Allowed : 17.09 % Favored : 81.32 % 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: 2.15 (0.26), residues: 1113 helix: 3.19 (0.25), residues: 391 sheet: 0.41 (0.31), residues: 256 loop : 0.58 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.011 0.001 PHE R 434 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8434 (mttt) cc_final: 0.8048 (mtmt) REVERT: A 82 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7788 (t-170) REVERT: A 208 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7366 (mtm180) REVERT: A 217 CYS cc_start: 0.8218 (m) cc_final: 0.7992 (t) REVERT: B 219 ARG cc_start: 0.8502 (mtt-85) cc_final: 0.8197 (mmt90) REVERT: B 258 ASP cc_start: 0.8793 (t70) cc_final: 0.8479 (t0) REVERT: B 327 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.8859 (p) REVERT: E 43 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7669 (mtpt) REVERT: E 174 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8773 (tt) REVERT: E 213 THR cc_start: 0.8621 (p) cc_final: 0.8235 (t) REVERT: R 57 LYS cc_start: 0.7839 (mttt) cc_final: 0.7278 (pttp) REVERT: R 218 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7404 (mtm110) REVERT: R 470 LEU cc_start: 0.8147 (tt) cc_final: 0.7922 (tp) outliers start: 15 outliers final: 11 residues processed: 144 average time/residue: 1.2339 time to fit residues: 190.0506 Evaluate side-chains 146 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 209 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain R residue 441 CYS Chi-restraints excluded: chain R residue 454 ILE Chi-restraints excluded: chain R residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 71 optimal weight: 0.0040 chunk 47 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 16 ASN R 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110603 restraints weight = 10967.621| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.01 r_work: 0.3132 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9187 Z= 0.139 Angle : 0.491 8.659 12486 Z= 0.253 Chirality : 0.040 0.153 1419 Planarity : 0.003 0.041 1551 Dihedral : 5.382 56.714 1564 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.80 % Allowed : 16.88 % Favored : 81.32 % 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: 2.16 (0.26), residues: 1113 helix: 3.23 (0.25), residues: 391 sheet: 0.39 (0.31), residues: 272 loop : 0.57 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.012 0.001 PHE A 74 TYR 0.017 0.001 TYR E 190 ARG 0.004 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7758.05 seconds wall clock time: 137 minutes 59.96 seconds (8279.96 seconds total)