Starting phenix.real_space_refine on Tue Jun 10 21:56:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdv_60014/06_2025/8zdv_60014.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdv_60014/06_2025/8zdv_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_60014/06_2025/8zdv_60014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdv_60014/06_2025/8zdv_60014.map" model { file = "/net/cci-nas-00/data/ceres_data/8zdv_60014/06_2025/8zdv_60014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdv_60014/06_2025/8zdv_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-5710/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: 6.63, per 1000 atoms: 0.54 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: 3.14 Conformation dependent library (CDL) restraints added in 1.6 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: 1.47 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: 3.50 Time building geometry restraints manager: 3.70 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 1.090 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.430 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.880 ------------------------------------------------------------------------------- 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 12517 Z= 0.387 Angle : 0.948 16.656 17015 Z= 0.526 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 Details of bonding type rmsd link_BETA2-3 : bond 0.03223 ( 3) link_BETA2-3 : angle 10.59417 ( 9) link_NAG-ASN : bond 0.01321 ( 15) link_NAG-ASN : angle 5.92344 ( 45) link_BETA1-2 : bond 0.00932 ( 3) link_BETA1-2 : angle 1.81207 ( 9) link_BETA1-4 : bond 0.00647 ( 9) link_BETA1-4 : angle 3.94894 ( 27) link_ALPHA1-3 : bond 0.01450 ( 3) link_ALPHA1-3 : angle 3.59820 ( 9) hydrogen bonds : bond 0.21165 ( 447) hydrogen bonds : angle 7.41986 ( 1323) SS BOND : bond 0.00636 ( 4) SS BOND : angle 3.23516 ( 8) covalent geometry : bond 0.00605 (12480) covalent geometry : angle 0.84373 (16908) *********************** 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 : 1.364 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: 1.1410 time to fit residues: 296.8350 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 : 1.489 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.173304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141762 restraints weight = 12520.563| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.73 r_work: 0.3477 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.004 0.037 12517 Z= 0.157 Angle : 0.726 11.883 17015 Z= 0.335 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 Details of bonding type rmsd link_BETA2-3 : bond 0.01287 ( 3) link_BETA2-3 : angle 3.76069 ( 9) link_NAG-ASN : bond 0.01007 ( 15) link_NAG-ASN : angle 5.24433 ( 45) link_BETA1-2 : bond 0.01348 ( 3) link_BETA1-2 : angle 2.84832 ( 9) link_BETA1-4 : bond 0.01276 ( 9) link_BETA1-4 : angle 3.53451 ( 27) link_ALPHA1-3 : bond 0.00922 ( 3) link_ALPHA1-3 : angle 1.79798 ( 9) hydrogen bonds : bond 0.04793 ( 447) hydrogen bonds : angle 5.55204 ( 1323) SS BOND : bond 0.00147 ( 4) SS BOND : angle 1.37709 ( 8) covalent geometry : bond 0.00348 (12480) covalent geometry : angle 0.65070 (16908) *********************** 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 : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 304 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6568 (mp0) REVERT: B 310 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8259 (mttt) REVERT: A 280 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7461 (mttt) REVERT: A 310 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8212 (mttt) REVERT: C 21 ASN cc_start: 0.7374 (p0) cc_final: 0.7134 (p0) REVERT: C 321 ARG cc_start: 0.6552 (mtm-85) cc_final: 0.6221 (mtm-85) REVERT: G 17 MET cc_start: 0.6677 (ttp) cc_final: 0.6335 (ttp) REVERT: G 69 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: G 128 ASP cc_start: 0.7613 (p0) cc_final: 0.7019 (t0) REVERT: H 128 ASP cc_start: 0.7487 (p0) cc_final: 0.6885 (t0) REVERT: I 75 ARG cc_start: 0.8346 (mmt90) cc_final: 0.7967 (mmm-85) REVERT: I 128 ASP cc_start: 0.7470 (p0) cc_final: 0.6986 (t0) outliers start: 23 outliers final: 7 residues processed: 199 average time/residue: 1.3094 time to fit residues: 282.0977 Evaluate side-chains 166 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 280 LYS 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 105 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 C 193 ASN H 15 GLN H 42 GLN I 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138730 restraints weight = 12629.106| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.69 r_work: 0.3403 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12517 Z= 0.171 Angle : 0.691 11.499 17015 Z= 0.327 Chirality : 0.048 0.394 1905 Planarity : 0.004 0.035 2163 Dihedral : 9.525 86.275 2298 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.94 % Allowed : 11.91 % 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: -0.50 (0.21), residues: 1461 helix: 1.28 (0.26), residues: 378 sheet: -0.13 (0.34), residues: 249 loop : -1.20 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 84 HIS 0.006 0.002 HIS A 18 PHE 0.020 0.002 PHE C 148 TYR 0.012 0.002 TYR G 119 ARG 0.004 0.000 ARG C 227 Details of bonding type rmsd link_BETA2-3 : bond 0.00916 ( 3) link_BETA2-3 : angle 3.96630 ( 9) link_NAG-ASN : bond 0.00927 ( 15) link_NAG-ASN : angle 5.19529 ( 45) link_BETA1-2 : bond 0.00650 ( 3) link_BETA1-2 : angle 1.08760 ( 9) link_BETA1-4 : bond 0.00845 ( 9) link_BETA1-4 : angle 2.59445 ( 27) link_ALPHA1-3 : bond 0.00644 ( 3) link_ALPHA1-3 : angle 1.65598 ( 9) hydrogen bonds : bond 0.04230 ( 447) hydrogen bonds : angle 5.25990 ( 1323) SS BOND : bond 0.00183 ( 4) SS BOND : angle 1.28161 ( 8) covalent geometry : bond 0.00396 (12480) covalent geometry : angle 0.62209 (16908) *********************** 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 223 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 310 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8375 (mttt) REVERT: A 310 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8372 (mttt) REVERT: C 112 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8518 (mt) REVERT: G 69 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7743 (mm-30) REVERT: G 128 ASP cc_start: 0.7735 (p0) cc_final: 0.7002 (t0) REVERT: G 145 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7076 (t0) REVERT: H 42 GLN cc_start: 0.7380 (tp40) cc_final: 0.7178 (tp-100) REVERT: H 128 ASP cc_start: 0.7571 (p0) cc_final: 0.6816 (t0) REVERT: I 118 LEU cc_start: 0.7793 (mp) cc_final: 0.7571 (mt) REVERT: I 128 ASP cc_start: 0.7677 (p0) cc_final: 0.7135 (t0) REVERT: I 145 ASP cc_start: 0.7332 (t70) cc_final: 0.7129 (t0) outliers start: 38 outliers final: 12 residues processed: 212 average time/residue: 1.2378 time to fit residues: 284.5260 Evaluate side-chains 178 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 G residue 145 ASP 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 144 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 0.0020 chunk 57 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- 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 A 278 ASN C 193 ASN C 222 GLN G 25 HIS H 15 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.167505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133562 restraints weight = 13282.633| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.89 r_work: 0.3433 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12517 Z= 0.138 Angle : 0.640 13.048 17015 Z= 0.303 Chirality : 0.046 0.446 1905 Planarity : 0.003 0.035 2163 Dihedral : 8.729 85.387 2298 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.78 % Allowed : 12.99 % Favored : 84.22 % 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: -0.40 (0.21), residues: 1461 helix: 1.35 (0.26), residues: 378 sheet: -0.13 (0.34), residues: 249 loop : -1.10 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 127 HIS 0.004 0.001 HIS B 18 PHE 0.015 0.002 PHE C 118 TYR 0.009 0.001 TYR G 119 ARG 0.001 0.000 ARG G 106 Details of bonding type rmsd link_BETA2-3 : bond 0.00872 ( 3) link_BETA2-3 : angle 4.05883 ( 9) link_NAG-ASN : bond 0.01214 ( 15) link_NAG-ASN : angle 5.02606 ( 45) link_BETA1-2 : bond 0.00525 ( 3) link_BETA1-2 : angle 1.03037 ( 9) link_BETA1-4 : bond 0.00927 ( 9) link_BETA1-4 : angle 2.18728 ( 27) link_ALPHA1-3 : bond 0.00764 ( 3) link_ALPHA1-3 : angle 1.36436 ( 9) hydrogen bonds : bond 0.03909 ( 447) hydrogen bonds : angle 5.11024 ( 1323) SS BOND : bond 0.00200 ( 4) SS BOND : angle 1.12505 ( 8) covalent geometry : bond 0.00311 (12480) covalent geometry : angle 0.57089 (16908) *********************** 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 216 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 LYS cc_start: 0.8699 (tppt) cc_final: 0.8042 (tppt) REVERT: B 280 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7616 (mttt) REVERT: B 310 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8227 (mttt) REVERT: A 310 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8229 (mttt) REVERT: G 128 ASP cc_start: 0.7712 (p0) cc_final: 0.6917 (t0) REVERT: H 128 ASP cc_start: 0.7582 (p0) cc_final: 0.6772 (t0) REVERT: H 148 CYS cc_start: 0.6773 (OUTLIER) cc_final: 0.5229 (m) REVERT: I 128 ASP cc_start: 0.7647 (p0) cc_final: 0.6995 (t0) outliers start: 36 outliers final: 12 residues processed: 207 average time/residue: 1.1939 time to fit residues: 269.0215 Evaluate side-chains 169 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 A residue 240 ASP 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 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 51 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 20 optimal weight: 0.0020 chunk 84 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN C 193 ASN G 114 ASN H 42 GLN H 114 ASN I 25 HIS I 42 GLN I 114 ASN I 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130203 restraints weight = 13391.604| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.88 r_work: 0.3390 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12517 Z= 0.211 Angle : 0.699 11.482 17015 Z= 0.336 Chirality : 0.048 0.437 1905 Planarity : 0.004 0.037 2163 Dihedral : 8.702 89.633 2298 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.17 % Allowed : 14.15 % Favored : 82.68 % 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: -0.58 (0.21), residues: 1461 helix: 1.17 (0.26), residues: 384 sheet: -0.23 (0.34), residues: 249 loop : -1.22 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 127 HIS 0.008 0.002 HIS A 18 PHE 0.016 0.002 PHE B 148 TYR 0.014 0.002 TYR B 168 ARG 0.003 0.000 ARG G 76 Details of bonding type rmsd link_BETA2-3 : bond 0.00875 ( 3) link_BETA2-3 : angle 4.55613 ( 9) link_NAG-ASN : bond 0.00930 ( 15) link_NAG-ASN : angle 4.95318 ( 45) link_BETA1-2 : bond 0.00617 ( 3) link_BETA1-2 : angle 0.93523 ( 9) link_BETA1-4 : bond 0.00822 ( 9) link_BETA1-4 : angle 1.98615 ( 27) link_ALPHA1-3 : bond 0.00568 ( 3) link_ALPHA1-3 : angle 1.49393 ( 9) hydrogen bonds : bond 0.04105 ( 447) hydrogen bonds : angle 5.25826 ( 1323) SS BOND : bond 0.00371 ( 4) SS BOND : angle 1.09176 ( 8) covalent geometry : bond 0.00501 (12480) covalent geometry : angle 0.63790 (16908) *********************** 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 212 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 LYS cc_start: 0.8705 (tppt) cc_final: 0.8066 (tppt) REVERT: B 310 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8267 (mttt) REVERT: A 292 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7933 (mmt) REVERT: A 310 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8264 (mttt) REVERT: G 128 ASP cc_start: 0.7734 (p0) cc_final: 0.6933 (t0) REVERT: H 128 ASP cc_start: 0.7683 (p0) cc_final: 0.6822 (t0) REVERT: H 148 CYS cc_start: 0.6634 (OUTLIER) cc_final: 0.4802 (m) REVERT: I 37 ASP cc_start: 0.6375 (OUTLIER) cc_final: 0.5926 (m-30) REVERT: I 42 GLN cc_start: 0.7412 (tp40) cc_final: 0.7150 (tp-100) REVERT: I 128 ASP cc_start: 0.7689 (p0) cc_final: 0.7008 (t0) REVERT: I 150 GLU cc_start: 0.7332 (pt0) cc_final: 0.6705 (pm20) outliers start: 41 outliers final: 20 residues processed: 198 average time/residue: 1.3944 time to fit residues: 300.7818 Evaluate side-chains 188 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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 292 MET Chi-restraints excluded: chain C residue 46 THR 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 C residue 285 VAL Chi-restraints excluded: chain G residue 18 VAL 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 86 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 H 15 GLN I 114 ASN I 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132400 restraints weight = 13425.839| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.86 r_work: 0.3433 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12517 Z= 0.127 Angle : 0.623 11.173 17015 Z= 0.297 Chirality : 0.046 0.416 1905 Planarity : 0.003 0.034 2163 Dihedral : 8.289 86.424 2298 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.47 % Allowed : 15.24 % 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: -0.39 (0.21), residues: 1461 helix: 1.36 (0.26), residues: 378 sheet: -0.20 (0.34), residues: 249 loop : -1.07 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.003 0.001 HIS A 18 PHE 0.013 0.001 PHE G 3 TYR 0.007 0.001 TYR G 157 ARG 0.002 0.000 ARG I 127 Details of bonding type rmsd link_BETA2-3 : bond 0.00795 ( 3) link_BETA2-3 : angle 4.11586 ( 9) link_NAG-ASN : bond 0.01307 ( 15) link_NAG-ASN : angle 4.52629 ( 45) link_BETA1-2 : bond 0.00409 ( 3) link_BETA1-2 : angle 0.84469 ( 9) link_BETA1-4 : bond 0.00958 ( 9) link_BETA1-4 : angle 2.12258 ( 27) link_ALPHA1-3 : bond 0.00531 ( 3) link_ALPHA1-3 : angle 1.41222 ( 9) hydrogen bonds : bond 0.03756 ( 447) hydrogen bonds : angle 5.04363 ( 1323) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.78451 ( 8) covalent geometry : bond 0.00281 (12480) covalent geometry : angle 0.56358 (16908) *********************** 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 208 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 LYS cc_start: 0.8665 (tppt) cc_final: 0.7951 (tppt) REVERT: B 310 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8223 (mttt) REVERT: A 292 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7707 (mmt) REVERT: A 310 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8215 (mttt) REVERT: C 112 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8436 (mt) REVERT: G 128 ASP cc_start: 0.7748 (p0) cc_final: 0.6905 (t0) REVERT: H 118 LEU cc_start: 0.7561 (mp) cc_final: 0.7356 (mp) REVERT: H 128 ASP cc_start: 0.7667 (p0) cc_final: 0.6799 (t0) REVERT: H 148 CYS cc_start: 0.6566 (OUTLIER) cc_final: 0.4680 (m) REVERT: I 37 ASP cc_start: 0.6179 (OUTLIER) cc_final: 0.5873 (m-30) REVERT: I 42 GLN cc_start: 0.7556 (tp40) cc_final: 0.7262 (tp-100) REVERT: I 118 LEU cc_start: 0.7484 (mp) cc_final: 0.7234 (mt) REVERT: I 128 ASP cc_start: 0.7706 (p0) cc_final: 0.7022 (t0) REVERT: I 150 GLU cc_start: 0.7196 (pt0) cc_final: 0.6609 (pm20) outliers start: 32 outliers final: 15 residues processed: 201 average time/residue: 1.3504 time to fit residues: 296.7746 Evaluate side-chains 180 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.541 ------------------------------------------------------------------------------- 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 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 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 73 LEU 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 146 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 102 optimal weight: 0.0470 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- 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 I 114 ASN I 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.166501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132207 restraints weight = 13423.130| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.93 r_work: 0.3436 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12517 Z= 0.147 Angle : 0.633 11.182 17015 Z= 0.306 Chirality : 0.046 0.418 1905 Planarity : 0.003 0.034 2163 Dihedral : 8.076 86.031 2298 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.86 % Allowed : 15.55 % 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: -0.51 (0.21), residues: 1461 helix: 1.38 (0.26), residues: 378 sheet: -0.42 (0.35), residues: 219 loop : -1.13 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 127 HIS 0.005 0.001 HIS B 276 PHE 0.013 0.002 PHE G 3 TYR 0.015 0.001 TYR H 119 ARG 0.002 0.000 ARG G 106 Details of bonding type rmsd link_BETA2-3 : bond 0.00733 ( 3) link_BETA2-3 : angle 4.34249 ( 9) link_NAG-ASN : bond 0.01222 ( 15) link_NAG-ASN : angle 4.49369 ( 45) link_BETA1-2 : bond 0.00420 ( 3) link_BETA1-2 : angle 0.84131 ( 9) link_BETA1-4 : bond 0.00904 ( 9) link_BETA1-4 : angle 1.94276 ( 27) link_ALPHA1-3 : bond 0.00453 ( 3) link_ALPHA1-3 : angle 1.44524 ( 9) hydrogen bonds : bond 0.03766 ( 447) hydrogen bonds : angle 5.02620 ( 1323) SS BOND : bond 0.00228 ( 4) SS BOND : angle 1.83128 ( 8) covalent geometry : bond 0.00335 (12480) covalent geometry : angle 0.57438 (16908) *********************** 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 211 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 LYS cc_start: 0.8623 (tppt) cc_final: 0.7938 (tppt) REVERT: B 310 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8231 (mttt) REVERT: A 310 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8212 (mttt) REVERT: C 112 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8487 (mt) REVERT: G 128 ASP cc_start: 0.7751 (p0) cc_final: 0.6860 (t0) REVERT: H 118 LEU cc_start: 0.7565 (mp) cc_final: 0.7215 (mt) REVERT: H 128 ASP cc_start: 0.7718 (p0) cc_final: 0.6824 (t0) REVERT: H 148 CYS cc_start: 0.6504 (OUTLIER) cc_final: 0.4585 (m) REVERT: I 37 ASP cc_start: 0.6197 (OUTLIER) cc_final: 0.5891 (m-30) REVERT: I 128 ASP cc_start: 0.7731 (p0) cc_final: 0.7063 (t0) REVERT: I 150 GLU cc_start: 0.7157 (pt0) cc_final: 0.6580 (pm20) outliers start: 37 outliers final: 19 residues processed: 199 average time/residue: 1.2144 time to fit residues: 263.1303 Evaluate side-chains 186 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 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 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 18 VAL Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 73 LEU 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 20 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 0.0370 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 12 optimal weight: 0.0170 chunk 59 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- 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 I 81 ASN I 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.168097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133520 restraints weight = 13395.242| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.82 r_work: 0.3450 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12517 Z= 0.119 Angle : 0.606 10.870 17015 Z= 0.291 Chirality : 0.045 0.411 1905 Planarity : 0.003 0.033 2163 Dihedral : 7.793 84.097 2298 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.24 % Allowed : 16.32 % Favored : 81.44 % 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: -0.39 (0.21), residues: 1461 helix: 1.49 (0.26), residues: 378 sheet: -0.38 (0.36), residues: 219 loop : -1.06 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.003 0.001 HIS G 25 PHE 0.011 0.001 PHE A 118 TYR 0.012 0.001 TYR H 119 ARG 0.001 0.000 ARG G 106 Details of bonding type rmsd link_BETA2-3 : bond 0.00686 ( 3) link_BETA2-3 : angle 4.15980 ( 9) link_NAG-ASN : bond 0.01211 ( 15) link_NAG-ASN : angle 4.47479 ( 45) link_BETA1-2 : bond 0.00400 ( 3) link_BETA1-2 : angle 0.83596 ( 9) link_BETA1-4 : bond 0.00852 ( 9) link_BETA1-4 : angle 1.86522 ( 27) link_ALPHA1-3 : bond 0.00419 ( 3) link_ALPHA1-3 : angle 1.45195 ( 9) hydrogen bonds : bond 0.03683 ( 447) hydrogen bonds : angle 4.94388 ( 1323) SS BOND : bond 0.00174 ( 4) SS BOND : angle 1.65905 ( 8) covalent geometry : bond 0.00261 (12480) covalent geometry : angle 0.54659 (16908) *********************** 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 202 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 LYS cc_start: 0.8596 (tppt) cc_final: 0.7899 (tppt) REVERT: B 310 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8153 (mttt) REVERT: A 310 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8195 (mttt) REVERT: C 112 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8427 (mt) REVERT: G 59 MET cc_start: 0.8042 (mmt) cc_final: 0.7807 (mmt) REVERT: G 128 ASP cc_start: 0.7767 (p0) cc_final: 0.6857 (t0) REVERT: H 118 LEU cc_start: 0.7496 (mp) cc_final: 0.7145 (mt) REVERT: H 128 ASP cc_start: 0.7735 (p0) cc_final: 0.6831 (t0) REVERT: H 148 CYS cc_start: 0.6471 (OUTLIER) cc_final: 0.4279 (m) REVERT: H 150 GLU cc_start: 0.7162 (pt0) cc_final: 0.6468 (pm20) REVERT: I 128 ASP cc_start: 0.7757 (p0) cc_final: 0.7043 (t0) REVERT: I 150 GLU cc_start: 0.7132 (pt0) cc_final: 0.6545 (pm20) outliers start: 29 outliers final: 16 residues processed: 193 average time/residue: 1.2322 time to fit residues: 259.5480 Evaluate side-chains 178 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 199 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 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 73 LEU 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 144 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 76 optimal weight: 0.0070 chunk 97 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- 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 G 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.167369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132660 restraints weight = 13418.327| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.85 r_work: 0.3437 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12517 Z= 0.134 Angle : 0.623 10.796 17015 Z= 0.302 Chirality : 0.046 0.410 1905 Planarity : 0.003 0.034 2163 Dihedral : 7.694 84.100 2298 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.47 % Allowed : 17.09 % Favored : 80.43 % 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: -0.47 (0.21), residues: 1461 helix: 1.35 (0.26), residues: 378 sheet: -0.39 (0.35), residues: 219 loop : -1.08 (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 18 PHE 0.014 0.002 PHE G 3 TYR 0.012 0.001 TYR H 119 ARG 0.002 0.000 ARG G 106 Details of bonding type rmsd link_BETA2-3 : bond 0.00671 ( 3) link_BETA2-3 : angle 4.28988 ( 9) link_NAG-ASN : bond 0.01169 ( 15) link_NAG-ASN : angle 4.47306 ( 45) link_BETA1-2 : bond 0.00395 ( 3) link_BETA1-2 : angle 0.80865 ( 9) link_BETA1-4 : bond 0.00830 ( 9) link_BETA1-4 : angle 1.80570 ( 27) link_ALPHA1-3 : bond 0.00360 ( 3) link_ALPHA1-3 : angle 1.48872 ( 9) hydrogen bonds : bond 0.03691 ( 447) hydrogen bonds : angle 4.95925 ( 1323) SS BOND : bond 0.00176 ( 4) SS BOND : angle 1.51899 ( 8) covalent geometry : bond 0.00303 (12480) covalent geometry : angle 0.56597 (16908) *********************** 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 197 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 310 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8170 (mttt) REVERT: A 112 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8139 (mt) REVERT: A 310 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8198 (mttt) REVERT: C 112 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8461 (mt) REVERT: G 59 MET cc_start: 0.8082 (mmt) cc_final: 0.7847 (mmt) REVERT: G 128 ASP cc_start: 0.7758 (p0) cc_final: 0.6846 (t0) REVERT: H 39 GLU cc_start: 0.6961 (mp0) cc_final: 0.6754 (pm20) REVERT: H 58 LYS cc_start: 0.7005 (tppp) cc_final: 0.5865 (tptp) REVERT: H 118 LEU cc_start: 0.7504 (mp) cc_final: 0.7156 (mt) REVERT: H 128 ASP cc_start: 0.7728 (p0) cc_final: 0.6861 (t0) REVERT: H 148 CYS cc_start: 0.6437 (OUTLIER) cc_final: 0.4223 (m) REVERT: H 150 GLU cc_start: 0.7273 (pt0) cc_final: 0.6526 (pm20) REVERT: I 128 ASP cc_start: 0.7751 (p0) cc_final: 0.7014 (t0) REVERT: I 150 GLU cc_start: 0.7151 (pt0) cc_final: 0.6547 (pm20) outliers start: 32 outliers final: 19 residues processed: 187 average time/residue: 1.2605 time to fit residues: 256.0929 Evaluate side-chains 176 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 235 THR Chi-restraints excluded: chain A residue 240 ASP 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 C residue 285 VAL Chi-restraints excluded: chain G residue 148 CYS 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 18 VAL Chi-restraints excluded: chain I residue 73 LEU 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 52 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 H 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130748 restraints weight = 13368.693| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.86 r_work: 0.3387 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12517 Z= 0.199 Angle : 0.695 10.776 17015 Z= 0.340 Chirality : 0.048 0.412 1905 Planarity : 0.004 0.036 2163 Dihedral : 7.978 88.806 2298 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.47 % Allowed : 17.17 % Favored : 80.36 % 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: -0.72 (0.20), residues: 1461 helix: 1.15 (0.26), residues: 384 sheet: -0.51 (0.35), residues: 219 loop : -1.28 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 69 HIS 0.007 0.001 HIS B 18 PHE 0.015 0.002 PHE B 148 TYR 0.015 0.002 TYR H 119 ARG 0.002 0.000 ARG I 68 Details of bonding type rmsd link_BETA2-3 : bond 0.00729 ( 3) link_BETA2-3 : angle 4.82753 ( 9) link_NAG-ASN : bond 0.01138 ( 15) link_NAG-ASN : angle 4.54046 ( 45) link_BETA1-2 : bond 0.00457 ( 3) link_BETA1-2 : angle 0.79844 ( 9) link_BETA1-4 : bond 0.00852 ( 9) link_BETA1-4 : angle 1.81869 ( 27) link_ALPHA1-3 : bond 0.00257 ( 3) link_ALPHA1-3 : angle 1.56688 ( 9) hydrogen bonds : bond 0.03942 ( 447) hydrogen bonds : angle 5.19030 ( 1323) SS BOND : bond 0.00281 ( 4) SS BOND : angle 1.73086 ( 8) covalent geometry : bond 0.00468 (12480) covalent geometry : angle 0.64105 (16908) ********************** 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 201 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 310 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8530 (mtmm) REVERT: A 310 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8248 (mttt) REVERT: C 262 LYS cc_start: 0.8488 (tttp) cc_final: 0.8151 (ttmt) REVERT: C 304 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6681 (pp20) REVERT: G 58 LYS cc_start: 0.7877 (tppp) cc_final: 0.7675 (mptp) REVERT: G 118 LEU cc_start: 0.7611 (mp) cc_final: 0.7399 (mt) REVERT: H 118 LEU cc_start: 0.7601 (mp) cc_final: 0.7253 (mt) REVERT: H 128 ASP cc_start: 0.7775 (p0) cc_final: 0.6883 (t0) REVERT: H 148 CYS cc_start: 0.6525 (OUTLIER) cc_final: 0.4299 (m) REVERT: H 150 GLU cc_start: 0.7288 (pt0) cc_final: 0.6516 (pm20) REVERT: I 42 GLN cc_start: 0.7525 (tp40) cc_final: 0.7279 (tp-100) REVERT: I 128 ASP cc_start: 0.7796 (p0) cc_final: 0.7045 (t0) REVERT: I 148 CYS cc_start: 0.6852 (OUTLIER) cc_final: 0.4568 (m) REVERT: I 150 GLU cc_start: 0.7265 (pt0) cc_final: 0.6663 (pm20) outliers start: 32 outliers final: 18 residues processed: 193 average time/residue: 1.2997 time to fit residues: 271.5887 Evaluate side-chains 182 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.779 ------------------------------------------------------------------------------- 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 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 235 THR Chi-restraints excluded: chain C residue 46 THR 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 C residue 285 VAL Chi-restraints excluded: chain G residue 148 CYS 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 73 LEU 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 7 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 H 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129964 restraints weight = 13387.051| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.86 r_work: 0.3411 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12517 Z= 0.178 Angle : 0.670 10.685 17015 Z= 0.326 Chirality : 0.047 0.406 1905 Planarity : 0.004 0.038 2163 Dihedral : 7.948 88.846 2298 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.09 % Allowed : 17.94 % Favored : 79.97 % 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: -0.76 (0.20), residues: 1461 helix: 1.14 (0.26), residues: 384 sheet: -0.53 (0.35), residues: 219 loop : -1.31 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 127 HIS 0.007 0.001 HIS B 18 PHE 0.014 0.002 PHE G 3 TYR 0.013 0.002 TYR H 119 ARG 0.002 0.000 ARG G 170 Details of bonding type rmsd link_BETA2-3 : bond 0.00729 ( 3) link_BETA2-3 : angle 4.63131 ( 9) link_NAG-ASN : bond 0.01108 ( 15) link_NAG-ASN : angle 4.49131 ( 45) link_BETA1-2 : bond 0.00407 ( 3) link_BETA1-2 : angle 0.81953 ( 9) link_BETA1-4 : bond 0.00836 ( 9) link_BETA1-4 : angle 1.82953 ( 27) link_ALPHA1-3 : bond 0.00237 ( 3) link_ALPHA1-3 : angle 1.57389 ( 9) hydrogen bonds : bond 0.03876 ( 447) hydrogen bonds : angle 5.19619 ( 1323) SS BOND : bond 0.00241 ( 4) SS BOND : angle 1.59430 ( 8) covalent geometry : bond 0.00417 (12480) covalent geometry : angle 0.61463 (16908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10098.59 seconds wall clock time: 177 minutes 57.99 seconds (10677.99 seconds total)