Starting phenix.real_space_refine on Mon Dec 30 03:25:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdv_60014/12_2024/8zdv_60014.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdv_60014/12_2024/8zdv_60014.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/8zdv_60014/12_2024/8zdv_60014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdv_60014/12_2024/8zdv_60014.map" model { file = "/net/cci-nas-00/data/ceres_data/8zdv_60014/12_2024/8zdv_60014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdv_60014/12_2024/8zdv_60014.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 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= 0.001 sd= 0.121 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 66 5.16 5 C 7653 2.51 5 N 2064 2.21 5 O 2427 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12210 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2535 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 301} Chain: "G" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1384 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, I, H, D, F Time building chain proxies: 6.87, per 1000 atoms: 0.56 Number of scatterers: 12210 At special positions: 0 Unit cell: (89.1586, 91.307, 147.165, 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 66 16.00 O 2427 8.00 N 2064 7.00 C 7653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " BETA1-2 " MAN D 4 " - " NAG D 5 " " MAN E 4 " - " NAG E 5 " " MAN F 4 " - " NAG F 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG D 5 " - " GAL D 6 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG E 5 " - " GAL E 6 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG F 5 " - " GAL F 6 " BETA2-3 " GAL D 6 " - " SIA D 7 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL E 6 " - " SIA E 7 " " GAL F 6 " - " SIA F 7 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 289 " " NAG B 401 " - " ASN B 21 " " NAG B 402 " - " ASN B 33 " " NAG B 403 " - " ASN B 289 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 289 " " NAG D 1 " - " ASN B 169 " " NAG E 1 " - " ASN C 169 " " NAG F 1 " - " ASN A 169 " " NAG G 201 " - " ASN G 154 " " NAG H 201 " - " ASN H 154 " " NAG I 201 " - " ASN I 154 " Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 1.7 seconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 33 sheets defined 27.9% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 125 through 127 removed outlier: 3.750A pdb=" N TRP B 127 " --> pdb=" O LYS B 125A" (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 127 removed outlier: 3.750A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 125 through 127 removed outlier: 3.749A pdb=" N TRP C 127 " --> pdb=" O LYS C 125A" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'G' and resid 37 through 60 Processing helix chain 'G' and resid 71 through 73 No H-bonds generated for 'chain 'G' and resid 71 through 73' Processing helix chain 'G' and resid 74 through 127 Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.622A pdb=" N MET G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 170 removed outlier: 3.927A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU G 165 " --> pdb=" O GLN G 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 60 Processing helix chain 'H' and resid 71 through 73 No H-bonds generated for 'chain 'H' and resid 71 through 73' Processing helix chain 'H' and resid 74 through 127 Processing helix chain 'H' and resid 145 through 155 removed outlier: 3.623A pdb=" N MET H 149 " --> pdb=" O ASP H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 170 removed outlier: 3.927A pdb=" N TYR H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY H 164 " --> pdb=" O PRO H 160 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 60 Processing helix chain 'I' and resid 71 through 73 No H-bonds generated for 'chain 'I' and resid 71 through 73' Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 145 through 155 removed outlier: 3.622A pdb=" N MET I 149 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 170 removed outlier: 3.927A pdb=" N TYR I 162 " --> pdb=" O ASP I 158 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU I 165 " --> pdb=" O GLN I 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'B' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'B' and resid 24 through 28 removed outlier: 4.127A pdb=" N GLU B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR B 28 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.395A pdb=" N LEU B 59 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.761A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 260A" --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N HIS B 117 " --> pdb=" O VAL B 260A" (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.761A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.319A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 168 removed outlier: 3.688A pdb=" N SER B 247 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AB3, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AB4, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AB5, first strand: chain 'A' and resid 24 through 28 removed outlier: 4.127A pdb=" N GLU A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR A 28 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 32 " --> pdb=" O THR A 28 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.396A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.761A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 260A" --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N HIS A 117 " --> pdb=" O VAL A 260A" (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.761A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.320A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 164 through 168 removed outlier: 3.689A pdb=" N SER A 247 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AC5, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AC6, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=AC7, first strand: chain 'C' and resid 24 through 28 removed outlier: 4.126A pdb=" N GLU C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR C 28 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS C 32 " --> pdb=" O THR C 28 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.395A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.761A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 260A" --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N HIS C 117 " --> pdb=" O VAL C 260A" (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.761A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.319A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 164 through 168 removed outlier: 3.688A pdb=" N SER C 247 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 281 through 282 477 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2067 1.32 - 1.44: 3447 1.44 - 1.57: 6870 1.57 - 1.70: 0 1.70 - 1.83: 96 Bond restraints: 12480 Sorted by residual: bond pdb=" CA SER A 146 " pdb=" CB SER A 146 " ideal model delta sigma weight residual 1.532 1.471 0.060 1.56e-02 4.11e+03 1.50e+01 bond pdb=" CA SER B 146 " pdb=" CB SER B 146 " ideal model delta sigma weight residual 1.532 1.471 0.060 1.56e-02 4.11e+03 1.49e+01 bond pdb=" CA SER C 146 " pdb=" CB SER C 146 " ideal model delta sigma weight residual 1.532 1.472 0.060 1.56e-02 4.11e+03 1.46e+01 bond pdb=" C SER A 221 " pdb=" O SER A 221 " ideal model delta sigma weight residual 1.234 1.188 0.046 1.22e-02 6.72e+03 1.42e+01 bond pdb=" C SER C 221 " pdb=" O SER C 221 " ideal model delta sigma weight residual 1.234 1.189 0.046 1.22e-02 6.72e+03 1.41e+01 ... (remaining 12475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 16029 1.84 - 3.69: 742 3.69 - 5.53: 107 5.53 - 7.37: 18 7.37 - 9.22: 12 Bond angle restraints: 16908 Sorted by residual: angle pdb=" N ALA A 138 " pdb=" CA ALA A 138 " pdb=" C ALA A 138 " ideal model delta sigma weight residual 112.89 105.48 7.41 1.24e+00 6.50e-01 3.57e+01 angle pdb=" N ALA B 138 " pdb=" CA ALA B 138 " pdb=" C ALA B 138 " ideal model delta sigma weight residual 112.89 105.50 7.39 1.24e+00 6.50e-01 3.55e+01 angle pdb=" N ALA C 138 " pdb=" CA ALA C 138 " pdb=" C ALA C 138 " ideal model delta sigma weight residual 112.89 105.51 7.38 1.24e+00 6.50e-01 3.54e+01 angle pdb=" N SER A 133 " pdb=" CA SER A 133 " pdb=" C SER A 133 " ideal model delta sigma weight residual 111.36 116.72 -5.36 1.09e+00 8.42e-01 2.42e+01 angle pdb=" N SER C 133 " pdb=" CA SER C 133 " pdb=" C SER C 133 " ideal model delta sigma weight residual 111.36 116.72 -5.36 1.09e+00 8.42e-01 2.42e+01 ... (remaining 16903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.16: 7300 20.16 - 40.31: 449 40.31 - 60.47: 87 60.47 - 80.62: 30 80.62 - 100.78: 18 Dihedral angle restraints: 7884 sinusoidal: 3621 harmonic: 4263 Sorted by residual: dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual -71.29 -172.07 100.78 1 3.00e+01 1.11e-03 1.27e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -172.06 100.77 1 3.00e+01 1.11e-03 1.27e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -172.05 100.76 1 3.00e+01 1.11e-03 1.27e+01 ... (remaining 7881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1825 0.117 - 0.234: 71 0.234 - 0.352: 0 0.352 - 0.469: 6 0.469 - 0.586: 3 Chirality restraints: 1905 Sorted by residual: chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-02 2.50e+03 8.59e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-02 2.50e+03 8.52e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-02 2.50e+03 8.52e+02 ... (remaining 1902 not shown) Planarity restraints: 2178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 5 " -0.341 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 5 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG E 5 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG E 5 " 0.511 2.00e-02 2.50e+03 pdb=" O7 NAG E 5 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 5 " 0.341 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG F 5 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG F 5 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG F 5 " -0.511 2.00e-02 2.50e+03 pdb=" O7 NAG F 5 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 5 " 0.341 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG D 5 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG D 5 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG D 5 " -0.511 2.00e-02 2.50e+03 pdb=" O7 NAG D 5 " 0.085 2.00e-02 2.50e+03 ... (remaining 2175 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 140 2.60 - 3.17: 10302 3.17 - 3.75: 18798 3.75 - 4.32: 27964 4.32 - 4.90: 45310 Nonbonded interactions: 102514 Sorted by model distance: nonbonded pdb=" SG CYS A 281 " pdb=" SG CYS A 305 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS C 281 " pdb=" SG CYS C 305 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS G 144 " pdb=" SG CYS G 148 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS H 144 " pdb=" SG CYS H 148 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS I 144 " pdb=" SG CYS I 148 " model vdw 2.029 3.760 ... (remaining 102509 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.710 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.290 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 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:14.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.006 0.070 12480 Z= 0.392 Angle : 0.844 9.217 16908 Z= 0.507 Chirality : 0.060 0.586 1905 Planarity : 0.012 0.291 2163 Dihedral : 14.604 100.781 5142 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1461 helix: 1.07 (0.26), residues: 387 sheet: 0.29 (0.37), residues: 219 loop : -1.28 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 14 HIS 0.009 0.001 HIS G 25 PHE 0.018 0.002 PHE B 148 TYR 0.018 0.001 TYR H 119 ARG 0.002 0.000 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 GLN cc_start: 0.6303 (pt0) cc_final: 0.5934 (pp30) REVERT: A 12 GLN cc_start: 0.6443 (pt0) cc_final: 0.5983 (pp30) REVERT: A 21 ASN cc_start: 0.7364 (p0) cc_final: 0.7119 (p0) REVERT: C 321 ARG cc_start: 0.6257 (mtm-85) cc_final: 0.6051 (mtm-85) REVERT: G 112 ASP cc_start: 0.7447 (t0) cc_final: 0.7233 (t0) REVERT: G 128 ASP cc_start: 0.7352 (p0) cc_final: 0.7043 (t0) REVERT: H 128 ASP cc_start: 0.7224 (p0) cc_final: 0.6900 (t0) REVERT: I 75 ARG cc_start: 0.7872 (mmt90) cc_final: 0.7613 (mmm-85) REVERT: I 128 ASP cc_start: 0.7213 (p0) cc_final: 0.6997 (t0) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 1.1458 time to fit residues: 297.7505 Evaluate side-chains 166 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 150 ASN B 193 ASN A 193 ASN A 278 ASN C 193 ASN G 60 ASN G 114 ASN H 15 GLN H 42 GLN H 60 ASN H 114 ASN I 25 HIS I 42 GLN I 60 ASN I 114 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12480 Z= 0.230 Angle : 0.651 10.153 16908 Z= 0.317 Chirality : 0.048 0.390 1905 Planarity : 0.003 0.036 2163 Dihedral : 10.957 83.160 2298 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.78 % Allowed : 10.05 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1461 helix: 1.24 (0.25), residues: 378 sheet: -0.13 (0.33), residues: 264 loop : -1.21 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 21 HIS 0.005 0.001 HIS B 18 PHE 0.017 0.002 PHE C 147 TYR 0.012 0.002 TYR G 119 ARG 0.003 0.000 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 310 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8114 (mttt) REVERT: C 21 ASN cc_start: 0.7145 (p0) cc_final: 0.6933 (p0) REVERT: C 321 ARG cc_start: 0.6454 (mtm-85) cc_final: 0.6111 (mtm-85) REVERT: G 17 MET cc_start: 0.6706 (ttp) cc_final: 0.6411 (ttp) REVERT: G 69 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: G 128 ASP cc_start: 0.7441 (p0) cc_final: 0.7023 (t0) REVERT: H 128 ASP cc_start: 0.7320 (p0) cc_final: 0.6885 (t0) REVERT: I 75 ARG cc_start: 0.8023 (mmt90) cc_final: 0.7726 (mmm-85) REVERT: I 128 ASP cc_start: 0.7333 (p0) cc_final: 0.7001 (t0) outliers start: 23 outliers final: 7 residues processed: 199 average time/residue: 1.3247 time to fit residues: 285.3890 Evaluate side-chains 163 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain I residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 193 ASN B 222 GLN A 193 ASN A 278 ASN C 193 ASN G 125 GLN H 15 GLN H 42 GLN I 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12480 Z= 0.254 Angle : 0.612 9.871 16908 Z= 0.306 Chirality : 0.047 0.392 1905 Planarity : 0.004 0.035 2163 Dihedral : 9.648 85.101 2298 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.71 % Allowed : 12.14 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.21), residues: 1461 helix: 1.29 (0.26), residues: 378 sheet: -0.27 (0.35), residues: 234 loop : -1.14 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 127 HIS 0.005 0.001 HIS B 18 PHE 0.020 0.002 PHE C 148 TYR 0.011 0.002 TYR A 195 ARG 0.004 0.000 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 310 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8186 (mttt) REVERT: C 112 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8470 (mt) REVERT: G 69 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7355 (mm-30) REVERT: G 128 ASP cc_start: 0.7579 (p0) cc_final: 0.7075 (t0) REVERT: H 128 ASP cc_start: 0.7412 (p0) cc_final: 0.6878 (t0) REVERT: I 59 MET cc_start: 0.7282 (mmt) cc_final: 0.7049 (mmt) REVERT: I 128 ASP cc_start: 0.7482 (p0) cc_final: 0.7116 (t0) outliers start: 35 outliers final: 12 residues processed: 206 average time/residue: 1.2806 time to fit residues: 286.8096 Evaluate side-chains 171 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 82 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 0.0370 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 127 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 193 ASN A 193 ASN C 193 ASN C 222 GLN G 25 HIS G 114 ASN H 15 GLN H 114 ASN I 114 ASN I 125 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12480 Z= 0.268 Angle : 0.611 6.569 16908 Z= 0.309 Chirality : 0.048 0.473 1905 Planarity : 0.004 0.034 2163 Dihedral : 8.921 87.780 2298 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.17 % Allowed : 12.45 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.21), residues: 1461 helix: 1.24 (0.26), residues: 378 sheet: -0.19 (0.34), residues: 249 loop : -1.20 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 127 HIS 0.006 0.001 HIS A 18 PHE 0.016 0.002 PHE C 118 TYR 0.011 0.002 TYR A 168 ARG 0.002 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 LYS cc_start: 0.8059 (tppt) cc_final: 0.7461 (tppt) REVERT: B 310 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8192 (mttt) REVERT: G 128 ASP cc_start: 0.7552 (p0) cc_final: 0.6971 (t0) REVERT: H 128 ASP cc_start: 0.7432 (p0) cc_final: 0.6825 (t0) REVERT: H 148 CYS cc_start: 0.6564 (OUTLIER) cc_final: 0.4946 (m) REVERT: I 128 ASP cc_start: 0.7583 (p0) cc_final: 0.7094 (t0) REVERT: I 150 GLU cc_start: 0.6780 (pt0) cc_final: 0.6538 (pm20) outliers start: 41 outliers final: 11 residues processed: 207 average time/residue: 1.3645 time to fit residues: 306.5001 Evaluate side-chains 173 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 82 LYS Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.0070 chunk 127 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN A 193 ASN C 193 ASN H 15 GLN H 42 GLN I 25 HIS I 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12480 Z= 0.297 Angle : 0.621 6.789 16908 Z= 0.315 Chirality : 0.048 0.430 1905 Planarity : 0.004 0.035 2163 Dihedral : 8.732 89.517 2298 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.25 % Allowed : 14.00 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1461 helix: 1.12 (0.26), residues: 384 sheet: -0.26 (0.34), residues: 249 loop : -1.26 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 127 HIS 0.008 0.001 HIS B 18 PHE 0.016 0.002 PHE G 3 TYR 0.014 0.002 TYR B 168 ARG 0.002 0.000 ARG H 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 LYS cc_start: 0.8059 (tppt) cc_final: 0.7444 (tppt) REVERT: B 310 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8180 (mttt) REVERT: A 292 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7981 (mmt) REVERT: C 310 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8219 (mttt) REVERT: G 69 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: G 128 ASP cc_start: 0.7545 (p0) cc_final: 0.6964 (t0) REVERT: H 128 ASP cc_start: 0.7529 (p0) cc_final: 0.6893 (t0) REVERT: H 148 CYS cc_start: 0.6618 (OUTLIER) cc_final: 0.4829 (m) REVERT: I 37 ASP cc_start: 0.6163 (OUTLIER) cc_final: 0.5837 (m-30) REVERT: I 75 ARG cc_start: 0.7929 (mmt90) cc_final: 0.7662 (mmm-85) REVERT: I 118 LEU cc_start: 0.7638 (mp) cc_final: 0.7427 (mt) REVERT: I 128 ASP cc_start: 0.7607 (p0) cc_final: 0.7085 (t0) REVERT: I 150 GLU cc_start: 0.6707 (pt0) cc_final: 0.6463 (pm20) outliers start: 42 outliers final: 20 residues processed: 203 average time/residue: 1.2661 time to fit residues: 278.9782 Evaluate side-chains 187 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 82 LYS Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.5980 chunk 127 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 142 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN B 40 GLN A 187 ASN G 62 GLN H 15 GLN I 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.003 0.030 12480 Z= 0.192 Angle : 0.557 8.071 16908 Z= 0.282 Chirality : 0.046 0.414 1905 Planarity : 0.003 0.034 2163 Dihedral : 8.252 86.728 2298 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.02 % Allowed : 14.69 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1461 helix: 1.33 (0.26), residues: 378 sheet: -0.23 (0.34), residues: 249 loop : -1.11 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 127 HIS 0.003 0.001 HIS B 18 PHE 0.013 0.001 PHE G 3 TYR 0.010 0.001 TYR B 17 ARG 0.002 0.000 ARG I 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 LYS cc_start: 0.8000 (tppt) cc_final: 0.7339 (tppt) REVERT: B 310 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8157 (mttt) REVERT: C 112 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8474 (mt) REVERT: G 69 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: G 128 ASP cc_start: 0.7586 (p0) cc_final: 0.6934 (t0) REVERT: H 128 ASP cc_start: 0.7538 (p0) cc_final: 0.6851 (t0) REVERT: H 148 CYS cc_start: 0.6657 (OUTLIER) cc_final: 0.4880 (m) REVERT: I 37 ASP cc_start: 0.6063 (OUTLIER) cc_final: 0.5807 (m-30) REVERT: I 128 ASP cc_start: 0.7604 (p0) cc_final: 0.7045 (t0) REVERT: I 150 GLU cc_start: 0.6705 (pt0) cc_final: 0.6485 (pm20) outliers start: 39 outliers final: 16 residues processed: 200 average time/residue: 1.1854 time to fit residues: 259.0194 Evaluate side-chains 180 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 0.0770 chunk 141 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN B 40 GLN A 187 ASN C 150 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 0.038 12480 Z= 0.181 Angle : 0.559 7.797 16908 Z= 0.282 Chirality : 0.046 0.417 1905 Planarity : 0.003 0.034 2163 Dihedral : 8.010 85.062 2298 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.55 % Allowed : 15.85 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1461 helix: 1.41 (0.26), residues: 378 sheet: -0.40 (0.35), residues: 219 loop : -1.10 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 127 HIS 0.004 0.001 HIS B 276 PHE 0.012 0.001 PHE A 118 TYR 0.017 0.001 TYR H 119 ARG 0.001 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 LYS cc_start: 0.7994 (tppt) cc_final: 0.7333 (tppt) REVERT: B 310 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8108 (mttt) REVERT: A 112 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8161 (mt) REVERT: A 292 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7444 (mmt) REVERT: C 112 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8463 (mt) REVERT: G 69 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: G 128 ASP cc_start: 0.7591 (p0) cc_final: 0.6931 (t0) REVERT: G 149 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.4776 (mmt) REVERT: H 128 ASP cc_start: 0.7566 (p0) cc_final: 0.6856 (t0) REVERT: H 148 CYS cc_start: 0.6526 (OUTLIER) cc_final: 0.4718 (m) REVERT: I 37 ASP cc_start: 0.5929 (OUTLIER) cc_final: 0.5725 (m-30) REVERT: I 118 LEU cc_start: 0.7537 (mp) cc_final: 0.7331 (mt) REVERT: I 128 ASP cc_start: 0.7654 (p0) cc_final: 0.7094 (t0) REVERT: I 150 GLU cc_start: 0.6718 (pt0) cc_final: 0.6480 (pm20) outliers start: 33 outliers final: 14 residues processed: 192 average time/residue: 1.2508 time to fit residues: 261.4924 Evaluate side-chains 179 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN B 40 GLN C 150 ASN G 15 GLN G 125 GLN H 42 GLN H 125 GLN I 81 ASN I 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.086 12480 Z= 0.693 Angle : 0.908 11.458 16908 Z= 0.461 Chirality : 0.058 0.434 1905 Planarity : 0.007 0.083 2163 Dihedral : 8.918 89.966 2298 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.48 % Allowed : 15.62 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1461 helix: 0.47 (0.25), residues: 384 sheet: -0.75 (0.32), residues: 249 loop : -1.67 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP A 69 HIS 0.017 0.003 HIS A 18 PHE 0.027 0.004 PHE B 148 TYR 0.022 0.004 TYR B 168 ARG 0.007 0.001 ARG G 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8250 (mmt) REVERT: C 187 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8171 (p0) REVERT: C 268 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7344 (ttm) REVERT: G 69 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7389 (mm-30) REVERT: H 128 ASP cc_start: 0.7593 (p0) cc_final: 0.6890 (t0) REVERT: H 148 CYS cc_start: 0.6637 (OUTLIER) cc_final: 0.4796 (m) REVERT: I 37 ASP cc_start: 0.6253 (OUTLIER) cc_final: 0.5968 (m-30) REVERT: I 75 ARG cc_start: 0.7997 (mmt90) cc_final: 0.7791 (mmm-85) REVERT: I 128 ASP cc_start: 0.7655 (p0) cc_final: 0.7087 (t0) REVERT: I 150 GLU cc_start: 0.6826 (pt0) cc_final: 0.6572 (pm20) outliers start: 45 outliers final: 17 residues processed: 196 average time/residue: 1.4176 time to fit residues: 299.8373 Evaluate side-chains 167 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain H residue 25 HIS Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12480 Z= 0.218 Angle : 0.639 8.869 16908 Z= 0.324 Chirality : 0.048 0.402 1905 Planarity : 0.003 0.040 2163 Dihedral : 8.400 87.986 2298 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.70 % Allowed : 18.48 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1461 helix: 0.87 (0.26), residues: 378 sheet: -0.69 (0.35), residues: 219 loop : -1.44 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 127 HIS 0.006 0.001 HIS I 25 PHE 0.015 0.002 PHE G 3 TYR 0.018 0.001 TYR H 119 ARG 0.002 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7970 (mmt) REVERT: A 307 LYS cc_start: 0.7401 (mmmt) cc_final: 0.7201 (mmmt) REVERT: C 31 GLU cc_start: 0.7065 (tt0) cc_final: 0.6815 (tt0) REVERT: H 128 ASP cc_start: 0.7549 (p0) cc_final: 0.6783 (t0) REVERT: H 148 CYS cc_start: 0.6510 (OUTLIER) cc_final: 0.4607 (m) REVERT: I 75 ARG cc_start: 0.7883 (mmt90) cc_final: 0.7620 (mmm-85) REVERT: I 128 ASP cc_start: 0.7614 (p0) cc_final: 0.7053 (t0) REVERT: I 150 GLU cc_start: 0.6798 (pt0) cc_final: 0.6544 (pm20) outliers start: 22 outliers final: 9 residues processed: 181 average time/residue: 1.3655 time to fit residues: 267.5678 Evaluate side-chains 162 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN B 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12480 Z= 0.366 Angle : 0.697 13.830 16908 Z= 0.354 Chirality : 0.050 0.413 1905 Planarity : 0.004 0.041 2163 Dihedral : 8.396 88.127 2298 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.93 % Allowed : 18.64 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.20), residues: 1461 helix: 0.81 (0.26), residues: 378 sheet: -0.68 (0.33), residues: 249 loop : -1.51 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 127 HIS 0.009 0.002 HIS B 18 PHE 0.016 0.003 PHE B 148 TYR 0.018 0.002 TYR H 119 ARG 0.002 0.000 ARG G 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8013 (mmt) REVERT: H 128 ASP cc_start: 0.7519 (p0) cc_final: 0.6743 (t0) REVERT: H 148 CYS cc_start: 0.6484 (OUTLIER) cc_final: 0.4575 (m) REVERT: I 75 ARG cc_start: 0.8019 (mmt90) cc_final: 0.7758 (mmm-85) REVERT: I 128 ASP cc_start: 0.7649 (p0) cc_final: 0.7076 (t0) REVERT: I 150 GLU cc_start: 0.6758 (pt0) cc_final: 0.6536 (pm20) outliers start: 25 outliers final: 14 residues processed: 171 average time/residue: 1.3911 time to fit residues: 257.0458 Evaluate side-chains 169 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN B 40 GLN C 187 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129858 restraints weight = 13406.907| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.87 r_work: 0.3399 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12480 Z= 0.255 Angle : 0.639 13.013 16908 Z= 0.325 Chirality : 0.048 0.406 1905 Planarity : 0.004 0.041 2163 Dihedral : 8.146 89.659 2298 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.78 % Allowed : 18.87 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1461 helix: 0.99 (0.26), residues: 378 sheet: -0.58 (0.33), residues: 249 loop : -1.42 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 127 HIS 0.006 0.001 HIS I 25 PHE 0.014 0.002 PHE G 3 TYR 0.015 0.002 TYR H 119 ARG 0.002 0.000 ARG G 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4683.16 seconds wall clock time: 85 minutes 40.63 seconds (5140.63 seconds total)