Starting phenix.real_space_refine on Wed Sep 17 23:13:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdv_60014/09_2025/8zdv_60014.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdv_60014/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zdv_60014/09_2025/8zdv_60014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdv_60014/09_2025/8zdv_60014.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zdv_60014/09_2025/8zdv_60014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdv_60014/09_2025/8zdv_60014.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12210 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" 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: "D" 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: "B" 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: A, C, H, I, E, F Time building chain proxies: 2.45, per 1000 atoms: 0.20 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=12, 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 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 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: 1.67 Conformation dependent library (CDL) restraints added in 846.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.46 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: 2.33 Time building geometry restraints manager: 1.89 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: 7316 20.16 - 40.31: 457 40.31 - 60.47: 87 60.47 - 80.62: 30 80.62 - 100.78: 18 Dihedral angle restraints: 7908 sinusoidal: 3645 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 7905 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: 2.03 - 2.60: 138 2.60 - 3.18: 10410 3.18 - 3.75: 18780 3.75 - 4.33: 27915 4.33 - 4.90: 45247 Nonbonded interactions: 102490 Sorted by model distance: 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 nonbonded pdb=" SG CYS C 14 " pdb=" SG CYS I 137 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS A 14 " pdb=" SG CYS H 137 " model vdw 2.033 3.760 ... (remaining 102485 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'E' 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: 1.590 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.600 ------------------------------------------------------------------------------- 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 12525 Z= 0.387 Angle : 0.952 16.656 17031 Z= 0.528 Chirality : 0.060 0.586 1905 Planarity : 0.012 0.291 2163 Dihedral : 14.604 100.781 5142 Min Nonbonded Distance : 2.029 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG C 227 TYR 0.018 0.001 TYR H 119 PHE 0.018 0.002 PHE B 148 TRP 0.006 0.001 TRP H 14 HIS 0.009 0.001 HIS G 25 Details of bonding type rmsd covalent geometry : bond 0.00605 (12480) covalent geometry : angle 0.84373 (16908) SS BOND : bond 0.00634 ( 12) SS BOND : angle 3.23764 ( 24) hydrogen bonds : bond 0.21165 ( 447) hydrogen bonds : angle 7.41986 ( 1323) link_ALPHA1-3 : bond 0.01450 ( 3) link_ALPHA1-3 : angle 3.59820 ( 9) 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_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) *********************** 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 : 0.387 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: 0.5950 (pp30) REVERT: A 12 GLN cc_start: 0.6443 (pt0) cc_final: 0.5995 (pp30) REVERT: A 21 ASN cc_start: 0.7364 (p0) cc_final: 0.7118 (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: 0.7230 (t0) REVERT: G 128 ASP cc_start: 0.7352 (p0) cc_final: 0.7044 (t0) REVERT: H 128 ASP cc_start: 0.7224 (p0) cc_final: 0.6902 (t0) REVERT: I 75 ARG cc_start: 0.7872 (mmt90) cc_final: 0.7612 (mmm-85) REVERT: I 128 ASP cc_start: 0.7213 (p0) cc_final: 0.6999 (t0) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.5642 time to fit residues: 145.9000 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 : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 15 GLN G 60 ASN G 114 ASN H 15 GLN H 42 GLN H 60 ASN H 114 ASN 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 = 0.3961 r_free = 0.3961 target = 0.171896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140157 restraints weight = 12638.899| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.73 r_work: 0.3408 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12525 Z= 0.172 Angle : 0.746 11.649 17031 Z= 0.346 Chirality : 0.049 0.394 1905 Planarity : 0.004 0.036 2163 Dihedral : 10.859 83.517 2298 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.86 % Allowed : 9.82 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.21), residues: 1461 helix: 1.14 (0.25), residues: 378 sheet: 0.22 (0.35), residues: 234 loop : -1.25 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 75 TYR 0.014 0.002 TYR C 195 PHE 0.018 0.003 PHE C 148 TRP 0.009 0.002 TRP I 21 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00386 (12480) covalent geometry : angle 0.67030 (16908) SS BOND : bond 0.00201 ( 12) SS BOND : angle 1.32678 ( 24) hydrogen bonds : bond 0.04472 ( 447) hydrogen bonds : angle 5.55579 ( 1323) link_ALPHA1-3 : bond 0.00703 ( 3) link_ALPHA1-3 : angle 1.83438 ( 9) link_BETA1-2 : bond 0.02118 ( 3) link_BETA1-2 : angle 3.04491 ( 9) link_BETA1-4 : bond 0.01247 ( 9) link_BETA1-4 : angle 3.71812 ( 27) link_BETA2-3 : bond 0.00377 ( 3) link_BETA2-3 : angle 3.58693 ( 9) link_NAG-ASN : bond 0.00944 ( 15) link_NAG-ASN : angle 5.21985 ( 45) *********************** 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 206 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 310 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8351 (mttt) REVERT: A 310 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8311 (mttt) REVERT: C 321 ARG cc_start: 0.6736 (mtm-85) cc_final: 0.6414 (mtm-85) REVERT: G 17 MET cc_start: 0.6932 (ttp) cc_final: 0.6528 (ttp) REVERT: G 69 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: G 128 ASP cc_start: 0.7733 (p0) cc_final: 0.7114 (t0) REVERT: H 128 ASP cc_start: 0.7600 (p0) cc_final: 0.6967 (t0) REVERT: I 58 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7326 (tppp) REVERT: I 75 ARG cc_start: 0.8432 (mmt90) cc_final: 0.8092 (mmm-85) REVERT: I 118 LEU cc_start: 0.7876 (mp) cc_final: 0.7582 (mt) REVERT: I 128 ASP cc_start: 0.7595 (p0) cc_final: 0.7119 (t0) outliers start: 24 outliers final: 8 residues processed: 195 average time/residue: 0.6067 time to fit residues: 128.1537 Evaluate side-chains 171 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 82 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 31 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 B 222 GLN A 193 ASN C 193 ASN G 15 GLN G 25 HIS G 114 ASN H 15 GLN H 42 GLN H 114 ASN I 42 GLN I 125 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134414 restraints weight = 12693.638| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.70 r_work: 0.3354 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12525 Z= 0.254 Angle : 0.797 12.193 17031 Z= 0.382 Chirality : 0.051 0.473 1905 Planarity : 0.005 0.050 2163 Dihedral : 9.894 89.479 2298 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.56 % Allowed : 11.52 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.20), residues: 1461 helix: 0.96 (0.26), residues: 378 sheet: 0.07 (0.35), residues: 219 loop : -1.37 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 321 TYR 0.015 0.002 TYR B 168 PHE 0.024 0.003 PHE B 148 TRP 0.013 0.002 TRP A 69 HIS 0.010 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00606 (12480) covalent geometry : angle 0.73236 (16908) SS BOND : bond 0.00409 ( 12) SS BOND : angle 1.36273 ( 24) hydrogen bonds : bond 0.04583 ( 447) hydrogen bonds : angle 5.53892 ( 1323) link_ALPHA1-3 : bond 0.00632 ( 3) link_ALPHA1-3 : angle 1.70808 ( 9) link_BETA1-2 : bond 0.00683 ( 3) link_BETA1-2 : angle 1.19922 ( 9) link_BETA1-4 : bond 0.00839 ( 9) link_BETA1-4 : angle 2.53788 ( 27) link_BETA2-3 : bond 0.01264 ( 3) link_BETA2-3 : angle 4.45910 ( 9) link_NAG-ASN : bond 0.00932 ( 15) link_NAG-ASN : angle 5.40068 ( 45) *********************** 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 232 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 LYS cc_start: 0.8638 (tppt) cc_final: 0.8038 (tppt) REVERT: B 292 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8075 (tpp) REVERT: B 310 LYS cc_start: 0.8890 (mtmt) cc_final: 0.8333 (mttt) REVERT: A 292 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8170 (mmt) REVERT: A 310 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8450 (mttt) REVERT: C 310 LYS cc_start: 0.8878 (mtmt) cc_final: 0.8402 (mttt) REVERT: G 58 LYS cc_start: 0.7780 (tptp) cc_final: 0.7502 (tppp) REVERT: G 69 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7805 (mm-30) REVERT: G 128 ASP cc_start: 0.7842 (p0) cc_final: 0.7017 (t0) REVERT: G 145 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.7091 (t0) REVERT: H 128 ASP cc_start: 0.7645 (p0) cc_final: 0.6893 (t0) REVERT: I 42 GLN cc_start: 0.7619 (tp40) cc_final: 0.7347 (tp-100) REVERT: I 75 ARG cc_start: 0.8376 (mmt90) cc_final: 0.8025 (mmm-85) REVERT: I 128 ASP cc_start: 0.7753 (p0) cc_final: 0.7139 (t0) outliers start: 46 outliers final: 12 residues processed: 220 average time/residue: 0.6434 time to fit residues: 152.7304 Evaluate side-chains 180 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 292 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 193 ASN 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 23 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 141 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 106 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 A 187 ASN A 193 ASN A 222 GLN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3925 r_free = 0.3925 target = 0.166812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133936 restraints weight = 13504.891| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.84 r_work: 0.3424 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12525 Z= 0.129 Angle : 0.646 11.189 17031 Z= 0.308 Chirality : 0.046 0.423 1905 Planarity : 0.003 0.036 2163 Dihedral : 9.147 88.577 2298 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.24 % Allowed : 14.00 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.21), residues: 1461 helix: 1.17 (0.26), residues: 378 sheet: 0.18 (0.36), residues: 219 loop : -1.15 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 76 TYR 0.010 0.001 TYR B 17 PHE 0.014 0.001 PHE A 118 TRP 0.010 0.001 TRP B 127 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00280 (12480) covalent geometry : angle 0.58596 (16908) SS BOND : bond 0.00181 ( 12) SS BOND : angle 0.90447 ( 24) hydrogen bonds : bond 0.03955 ( 447) hydrogen bonds : angle 5.26842 ( 1323) link_ALPHA1-3 : bond 0.00732 ( 3) link_ALPHA1-3 : angle 1.43518 ( 9) link_BETA1-2 : bond 0.00700 ( 3) link_BETA1-2 : angle 1.12250 ( 9) link_BETA1-4 : bond 0.01069 ( 9) link_BETA1-4 : angle 2.54491 ( 27) link_BETA2-3 : bond 0.00926 ( 3) link_BETA2-3 : angle 3.84364 ( 9) link_NAG-ASN : bond 0.01331 ( 15) link_NAG-ASN : angle 4.57268 ( 45) *********************** 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 214 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 LYS cc_start: 0.8678 (tppt) cc_final: 0.8009 (tppt) REVERT: B 310 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8232 (mttt) REVERT: A 310 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8229 (mttt) REVERT: C 112 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8422 (mt) REVERT: C 258 TYR cc_start: 0.7791 (m-80) cc_final: 0.7591 (m-80) REVERT: G 58 LYS cc_start: 0.7657 (tptp) cc_final: 0.7396 (mptm) REVERT: G 128 ASP cc_start: 0.7726 (p0) cc_final: 0.6915 (t0) REVERT: H 128 ASP cc_start: 0.7628 (p0) cc_final: 0.6797 (t0) REVERT: H 148 CYS cc_start: 0.6630 (OUTLIER) cc_final: 0.4780 (m) REVERT: I 42 GLN cc_start: 0.7523 (tp40) cc_final: 0.7285 (tp-100) REVERT: I 73 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8367 (mt) REVERT: I 75 ARG cc_start: 0.8275 (mmt90) cc_final: 0.7813 (mmm-85) REVERT: I 128 ASP cc_start: 0.7651 (p0) cc_final: 0.6998 (t0) outliers start: 29 outliers final: 10 residues processed: 208 average time/residue: 0.6036 time to fit residues: 135.9459 Evaluate side-chains 180 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 C residue 46 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 199 THR 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 13 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 222 GLN A 278 ASN C 193 ASN C 222 GLN G 125 GLN H 15 GLN H 42 GLN H 114 ASN H 125 GLN I 114 ASN I 125 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126480 restraints weight = 13658.362| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.83 r_work: 0.3342 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 12525 Z= 0.372 Angle : 0.878 11.496 17031 Z= 0.428 Chirality : 0.055 0.431 1905 Planarity : 0.006 0.068 2163 Dihedral : 9.346 89.670 2298 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.25 % Allowed : 14.46 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.20), residues: 1461 helix: 0.64 (0.25), residues: 378 sheet: -0.61 (0.33), residues: 249 loop : -1.56 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 68 TYR 0.019 0.003 TYR C 201 PHE 0.024 0.004 PHE B 148 TRP 0.017 0.003 TRP A 69 HIS 0.013 0.003 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00895 (12480) covalent geometry : angle 0.82241 (16908) SS BOND : bond 0.00732 ( 12) SS BOND : angle 1.31775 ( 24) hydrogen bonds : bond 0.04627 ( 447) hydrogen bonds : angle 5.77789 ( 1323) link_ALPHA1-3 : bond 0.00533 ( 3) link_ALPHA1-3 : angle 1.68340 ( 9) link_BETA1-2 : bond 0.00665 ( 3) link_BETA1-2 : angle 1.29200 ( 9) link_BETA1-4 : bond 0.00948 ( 9) link_BETA1-4 : angle 2.15106 ( 27) link_BETA2-3 : bond 0.00872 ( 3) link_BETA2-3 : angle 5.30075 ( 9) link_NAG-ASN : bond 0.01077 ( 15) link_NAG-ASN : angle 5.23584 ( 45) *********************** 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 227 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 310 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8318 (mttt) REVERT: A 227 ARG cc_start: 0.7367 (mtt-85) cc_final: 0.7107 (mtt180) REVERT: A 292 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8169 (mmt) REVERT: A 310 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8373 (mttt) REVERT: C 187 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8479 (p0) REVERT: C 262 LYS cc_start: 0.8602 (tttp) cc_final: 0.8262 (ttmt) REVERT: C 310 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8547 (mtmm) REVERT: G 58 LYS cc_start: 0.7857 (tptp) cc_final: 0.7520 (tppp) REVERT: H 128 ASP cc_start: 0.7746 (p0) cc_final: 0.6892 (t0) REVERT: H 148 CYS cc_start: 0.6723 (OUTLIER) cc_final: 0.4836 (m) REVERT: I 37 ASP cc_start: 0.6557 (OUTLIER) cc_final: 0.6078 (m-30) REVERT: I 42 GLN cc_start: 0.7497 (tp40) cc_final: 0.7235 (tp-100) REVERT: I 73 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8391 (mm) REVERT: I 75 ARG cc_start: 0.8405 (mmt90) cc_final: 0.7962 (mmm-85) REVERT: I 128 ASP cc_start: 0.7713 (p0) cc_final: 0.7008 (t0) outliers start: 55 outliers final: 21 residues processed: 212 average time/residue: 0.6482 time to fit residues: 148.3452 Evaluate side-chains 183 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain A residue 35 THR 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 264 ASP Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 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 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 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 21 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN C 12 GLN ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN H 125 GLN I 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.165617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130907 restraints weight = 13430.293| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.83 r_work: 0.3409 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12525 Z= 0.133 Angle : 0.643 10.732 17031 Z= 0.314 Chirality : 0.047 0.395 1905 Planarity : 0.003 0.037 2163 Dihedral : 8.709 89.245 2298 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.40 % Allowed : 16.94 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.21), residues: 1461 helix: 1.08 (0.26), residues: 378 sheet: -0.11 (0.38), residues: 189 loop : -1.29 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 127 TYR 0.011 0.001 TYR G 34 PHE 0.013 0.001 PHE G 3 TRP 0.012 0.001 TRP B 127 HIS 0.005 0.001 HIS I 25 Details of bonding type rmsd covalent geometry : bond 0.00291 (12480) covalent geometry : angle 0.59260 (16908) SS BOND : bond 0.00234 ( 12) SS BOND : angle 2.09537 ( 24) hydrogen bonds : bond 0.03875 ( 447) hydrogen bonds : angle 5.32218 ( 1323) link_ALPHA1-3 : bond 0.00493 ( 3) link_ALPHA1-3 : angle 1.46904 ( 9) link_BETA1-2 : bond 0.00419 ( 3) link_BETA1-2 : angle 0.86984 ( 9) link_BETA1-4 : bond 0.00983 ( 9) link_BETA1-4 : angle 2.20032 ( 27) link_BETA2-3 : bond 0.00872 ( 3) link_BETA2-3 : angle 4.02846 ( 9) link_NAG-ASN : bond 0.01222 ( 15) link_NAG-ASN : angle 3.94089 ( 45) *********************** 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 204 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7647 (mttt) REVERT: B 310 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8221 (mttt) REVERT: A 292 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7681 (mmt) REVERT: A 310 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8255 (mttt) REVERT: C 21 ASN cc_start: 0.7464 (p0) cc_final: 0.7216 (p0) REVERT: C 112 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8475 (mt) REVERT: G 58 LYS cc_start: 0.7901 (tptp) cc_final: 0.7566 (tppp) REVERT: G 83 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8122 (mmmm) REVERT: G 150 GLU cc_start: 0.7180 (pt0) cc_final: 0.6524 (pm20) REVERT: H 58 LYS cc_start: 0.7351 (tppp) cc_final: 0.6115 (tptp) REVERT: H 128 ASP cc_start: 0.7770 (p0) cc_final: 0.6890 (t0) REVERT: H 148 CYS cc_start: 0.6601 (OUTLIER) cc_final: 0.4654 (m) REVERT: I 37 ASP cc_start: 0.6246 (OUTLIER) cc_final: 0.5953 (m-30) REVERT: I 42 GLN cc_start: 0.7497 (tp40) cc_final: 0.7239 (tp-100) REVERT: I 73 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8358 (mt) REVERT: I 75 ARG cc_start: 0.8290 (mmt90) cc_final: 0.7845 (mmm-85) REVERT: I 128 ASP cc_start: 0.7714 (p0) cc_final: 0.7021 (t0) REVERT: I 150 GLU cc_start: 0.7177 (pt0) cc_final: 0.6584 (pm20) outliers start: 31 outliers final: 14 residues processed: 198 average time/residue: 0.6239 time to fit residues: 133.7126 Evaluate side-chains 187 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 A residue 88 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain G residue 128 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 82 LYS 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 14 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 146 optimal weight: 0.2980 chunk 122 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN C 12 GLN C 150 ASN G 62 GLN H 15 GLN H 42 GLN I 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131362 restraints weight = 13458.905| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.85 r_work: 0.3415 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12525 Z= 0.139 Angle : 0.623 10.677 17031 Z= 0.305 Chirality : 0.046 0.403 1905 Planarity : 0.003 0.035 2163 Dihedral : 8.320 87.856 2298 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.32 % Allowed : 17.40 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.21), residues: 1461 helix: 1.20 (0.26), residues: 378 sheet: -0.08 (0.38), residues: 189 loop : -1.24 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 106 TYR 0.012 0.001 TYR H 119 PHE 0.013 0.002 PHE G 3 TRP 0.011 0.001 TRP B 127 HIS 0.004 0.001 HIS I 25 Details of bonding type rmsd covalent geometry : bond 0.00312 (12480) covalent geometry : angle 0.57283 (16908) SS BOND : bond 0.00171 ( 12) SS BOND : angle 1.60595 ( 24) hydrogen bonds : bond 0.03845 ( 447) hydrogen bonds : angle 5.19246 ( 1323) link_ALPHA1-3 : bond 0.00442 ( 3) link_ALPHA1-3 : angle 1.46614 ( 9) link_BETA1-2 : bond 0.00437 ( 3) link_BETA1-2 : angle 0.84820 ( 9) link_BETA1-4 : bond 0.00929 ( 9) link_BETA1-4 : angle 2.01966 ( 27) link_BETA2-3 : bond 0.00766 ( 3) link_BETA2-3 : angle 4.20085 ( 9) link_NAG-ASN : bond 0.01265 ( 15) link_NAG-ASN : angle 3.96021 ( 45) *********************** 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 199 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7661 (mttt) REVERT: B 310 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8228 (mttt) REVERT: A 292 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7939 (mmt) REVERT: A 310 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8253 (mttt) REVERT: C 112 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8474 (mt) REVERT: G 58 LYS cc_start: 0.7867 (tptp) cc_final: 0.7646 (tppt) REVERT: G 83 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8216 (mmmm) REVERT: G 146 ASN cc_start: 0.6725 (m-40) cc_final: 0.6346 (t0) REVERT: G 150 GLU cc_start: 0.7214 (pt0) cc_final: 0.6528 (pm20) REVERT: H 58 LYS cc_start: 0.7237 (tppp) cc_final: 0.6038 (tptp) REVERT: H 128 ASP cc_start: 0.7776 (p0) cc_final: 0.6882 (t0) REVERT: H 148 CYS cc_start: 0.6634 (OUTLIER) cc_final: 0.4429 (m) REVERT: H 150 GLU cc_start: 0.7247 (pt0) cc_final: 0.6525 (pm20) REVERT: I 37 ASP cc_start: 0.6311 (OUTLIER) cc_final: 0.6009 (m-30) REVERT: I 42 GLN cc_start: 0.7443 (tp40) cc_final: 0.7184 (tp-100) REVERT: I 73 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8352 (mt) REVERT: I 75 ARG cc_start: 0.8267 (mmt90) cc_final: 0.7807 (mmm-85) REVERT: I 82 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8093 (ttpt) REVERT: I 128 ASP cc_start: 0.7742 (p0) cc_final: 0.7022 (t0) REVERT: I 150 GLU cc_start: 0.7150 (pt0) cc_final: 0.6596 (pm20) outliers start: 30 outliers final: 17 residues processed: 189 average time/residue: 0.5903 time to fit residues: 120.8096 Evaluate side-chains 179 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 A residue 264 ASP Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 128 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 82 LYS 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 72 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.164852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130838 restraints weight = 13457.005| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.89 r_work: 0.3393 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12525 Z= 0.185 Angle : 0.656 10.672 17031 Z= 0.322 Chirality : 0.047 0.403 1905 Planarity : 0.004 0.036 2163 Dihedral : 8.303 88.722 2298 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.71 % Allowed : 17.17 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.21), residues: 1461 helix: 1.15 (0.26), residues: 378 sheet: -0.11 (0.38), residues: 189 loop : -1.30 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 106 TYR 0.015 0.002 TYR H 119 PHE 0.016 0.002 PHE G 3 TRP 0.011 0.002 TRP B 127 HIS 0.007 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00434 (12480) covalent geometry : angle 0.60735 (16908) SS BOND : bond 0.00232 ( 12) SS BOND : angle 1.56928 ( 24) hydrogen bonds : bond 0.03926 ( 447) hydrogen bonds : angle 5.26569 ( 1323) link_ALPHA1-3 : bond 0.00374 ( 3) link_ALPHA1-3 : angle 1.51356 ( 9) link_BETA1-2 : bond 0.00435 ( 3) link_BETA1-2 : angle 0.81461 ( 9) link_BETA1-4 : bond 0.00923 ( 9) link_BETA1-4 : angle 1.99391 ( 27) link_BETA2-3 : bond 0.00782 ( 3) link_BETA2-3 : angle 4.47859 ( 9) link_NAG-ASN : bond 0.01208 ( 15) link_NAG-ASN : angle 3.98461 ( 45) *********************** 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 197 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7718 (mttt) REVERT: B 310 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8258 (mttt) REVERT: A 310 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8288 (mttt) REVERT: C 21 ASN cc_start: 0.7509 (p0) cc_final: 0.7252 (p0) REVERT: G 58 LYS cc_start: 0.7923 (tptp) cc_final: 0.7698 (tppt) REVERT: G 83 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8261 (mmmm) REVERT: G 150 GLU cc_start: 0.7228 (pt0) cc_final: 0.6544 (pm20) REVERT: H 58 LYS cc_start: 0.7284 (tppp) cc_final: 0.6055 (tptp) REVERT: H 128 ASP cc_start: 0.7753 (p0) cc_final: 0.6807 (t0) REVERT: H 148 CYS cc_start: 0.6690 (OUTLIER) cc_final: 0.4455 (m) REVERT: H 150 GLU cc_start: 0.7303 (pt0) cc_final: 0.6507 (pm20) REVERT: I 37 ASP cc_start: 0.6377 (OUTLIER) cc_final: 0.6031 (m-30) REVERT: I 42 GLN cc_start: 0.7435 (tp40) cc_final: 0.7198 (tp-100) REVERT: I 75 ARG cc_start: 0.8270 (mmt90) cc_final: 0.7810 (mmm-85) REVERT: I 128 ASP cc_start: 0.7770 (p0) cc_final: 0.7046 (t0) REVERT: I 150 GLU cc_start: 0.7142 (pt0) cc_final: 0.6579 (pm20) outliers start: 35 outliers final: 20 residues processed: 188 average time/residue: 0.6671 time to fit residues: 135.5041 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 : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 194 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 B residue 268 MET 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 264 ASP Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain G residue 128 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 82 LYS 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 34 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130468 restraints weight = 13493.873| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.85 r_work: 0.3394 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12525 Z= 0.177 Angle : 0.669 10.531 17031 Z= 0.328 Chirality : 0.047 0.399 1905 Planarity : 0.004 0.038 2163 Dihedral : 8.202 88.919 2298 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.47 % Allowed : 17.48 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.21), residues: 1461 helix: 1.12 (0.26), residues: 378 sheet: -0.04 (0.36), residues: 219 loop : -1.28 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 106 TYR 0.017 0.002 TYR H 119 PHE 0.014 0.002 PHE G 3 TRP 0.011 0.001 TRP B 127 HIS 0.007 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00412 (12480) covalent geometry : angle 0.62239 (16908) SS BOND : bond 0.00225 ( 12) SS BOND : angle 1.53537 ( 24) hydrogen bonds : bond 0.03889 ( 447) hydrogen bonds : angle 5.29557 ( 1323) link_ALPHA1-3 : bond 0.00315 ( 3) link_ALPHA1-3 : angle 1.53902 ( 9) link_BETA1-2 : bond 0.00429 ( 3) link_BETA1-2 : angle 0.80784 ( 9) link_BETA1-4 : bond 0.00902 ( 9) link_BETA1-4 : angle 1.97311 ( 27) link_BETA2-3 : bond 0.00751 ( 3) link_BETA2-3 : angle 4.51556 ( 9) link_NAG-ASN : bond 0.01167 ( 15) link_NAG-ASN : angle 3.94842 ( 45) *********************** 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 199 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8329 (mmt180) REVERT: B 280 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7712 (mttt) REVERT: B 310 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8259 (mttt) REVERT: A 292 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7818 (mmt) REVERT: A 310 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8298 (mttt) REVERT: C 21 ASN cc_start: 0.7515 (p0) cc_final: 0.7260 (p0) REVERT: G 58 LYS cc_start: 0.7945 (tptp) cc_final: 0.7723 (tppt) REVERT: G 83 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8248 (mmmm) REVERT: G 146 ASN cc_start: 0.6789 (m-40) cc_final: 0.6369 (t0) REVERT: G 150 GLU cc_start: 0.7281 (pt0) cc_final: 0.6542 (pm20) REVERT: H 128 ASP cc_start: 0.7757 (p0) cc_final: 0.6807 (t0) REVERT: H 145 ASP cc_start: 0.7512 (t70) cc_final: 0.7297 (t70) REVERT: H 148 CYS cc_start: 0.6609 (OUTLIER) cc_final: 0.4353 (m) REVERT: H 150 GLU cc_start: 0.7321 (pt0) cc_final: 0.6580 (pm20) REVERT: I 37 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.6034 (m-30) REVERT: I 75 ARG cc_start: 0.8266 (mmt90) cc_final: 0.7807 (mmm-85) REVERT: I 128 ASP cc_start: 0.7784 (p0) cc_final: 0.7043 (t0) REVERT: I 150 GLU cc_start: 0.7141 (pt0) cc_final: 0.6584 (pm20) outliers start: 32 outliers final: 21 residues processed: 191 average time/residue: 0.6931 time to fit residues: 142.7858 Evaluate side-chains 184 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 194 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 264 ASP Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 128 ASP 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 37 ASP Chi-restraints excluded: chain I residue 82 LYS 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 98 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.166107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132230 restraints weight = 13424.060| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.89 r_work: 0.3410 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12525 Z= 0.139 Angle : 0.631 10.426 17031 Z= 0.309 Chirality : 0.046 0.395 1905 Planarity : 0.003 0.038 2163 Dihedral : 7.979 86.827 2298 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.24 % Allowed : 17.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.21), residues: 1461 helix: 1.26 (0.26), residues: 378 sheet: -0.08 (0.38), residues: 189 loop : -1.22 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 106 TYR 0.014 0.001 TYR H 119 PHE 0.013 0.002 PHE G 3 TRP 0.011 0.001 TRP B 127 HIS 0.006 0.001 HIS I 25 Details of bonding type rmsd covalent geometry : bond 0.00316 (12480) covalent geometry : angle 0.58372 (16908) SS BOND : bond 0.00176 ( 12) SS BOND : angle 1.40360 ( 24) hydrogen bonds : bond 0.03801 ( 447) hydrogen bonds : angle 5.17900 ( 1323) link_ALPHA1-3 : bond 0.00325 ( 3) link_ALPHA1-3 : angle 1.53140 ( 9) link_BETA1-2 : bond 0.00368 ( 3) link_BETA1-2 : angle 0.81471 ( 9) link_BETA1-4 : bond 0.00869 ( 9) link_BETA1-4 : angle 1.97299 ( 27) link_BETA2-3 : bond 0.00756 ( 3) link_BETA2-3 : angle 4.28008 ( 9) link_NAG-ASN : bond 0.01131 ( 15) link_NAG-ASN : angle 3.87274 ( 45) ********************** 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 194 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8358 (mmt180) REVERT: B 310 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8255 (mttt) REVERT: A 310 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8269 (mttt) REVERT: C 21 ASN cc_start: 0.7530 (p0) cc_final: 0.7278 (p0) REVERT: C 112 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8341 (mt) REVERT: C 262 LYS cc_start: 0.8397 (tttp) cc_final: 0.8133 (ttmt) REVERT: G 58 LYS cc_start: 0.7885 (tptp) cc_final: 0.7676 (tppt) REVERT: G 83 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8237 (mmmm) REVERT: G 118 LEU cc_start: 0.7378 (mt) cc_final: 0.6653 (tp) REVERT: G 146 ASN cc_start: 0.6688 (m-40) cc_final: 0.6284 (t0) REVERT: G 150 GLU cc_start: 0.7277 (pt0) cc_final: 0.6514 (pm20) REVERT: H 39 GLU cc_start: 0.6926 (mp0) cc_final: 0.6708 (pm20) REVERT: H 58 LYS cc_start: 0.7316 (tppp) cc_final: 0.6038 (tptp) REVERT: H 128 ASP cc_start: 0.7752 (p0) cc_final: 0.6786 (t0) REVERT: H 145 ASP cc_start: 0.7489 (t70) cc_final: 0.7174 (t70) REVERT: H 150 GLU cc_start: 0.7346 (pt0) cc_final: 0.6585 (pm20) REVERT: I 37 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.5983 (m-30) REVERT: I 75 ARG cc_start: 0.8260 (mmt90) cc_final: 0.7795 (mmm-85) REVERT: I 82 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8083 (ttpt) REVERT: I 128 ASP cc_start: 0.7783 (p0) cc_final: 0.6993 (t0) REVERT: I 148 CYS cc_start: 0.6631 (OUTLIER) cc_final: 0.4365 (m) REVERT: I 150 GLU cc_start: 0.7139 (pt0) cc_final: 0.6552 (pm20) outliers start: 29 outliers final: 16 residues processed: 185 average time/residue: 0.7227 time to fit residues: 144.0845 Evaluate side-chains 184 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 149 ARG 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 235 THR Chi-restraints excluded: chain A residue 264 ASP 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 128 ASP 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 I residue 37 ASP Chi-restraints excluded: chain I residue 82 LYS 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 133 optimal weight: 10.0000 chunk 52 optimal weight: 0.0040 chunk 59 optimal weight: 4.9990 chunk 129 optimal weight: 0.0470 chunk 25 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.4090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.168544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135756 restraints weight = 13343.709| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.85 r_work: 0.3445 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12525 Z= 0.114 Angle : 0.591 10.339 17031 Z= 0.290 Chirality : 0.045 0.394 1905 Planarity : 0.003 0.037 2163 Dihedral : 7.557 82.215 2298 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.01 % Allowed : 18.64 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.21), residues: 1461 helix: 1.44 (0.26), residues: 378 sheet: 0.01 (0.38), residues: 189 loop : -1.09 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 106 TYR 0.017 0.001 TYR G 119 PHE 0.011 0.001 PHE H 110 TRP 0.013 0.001 TRP B 127 HIS 0.005 0.001 HIS I 25 Details of bonding type rmsd covalent geometry : bond 0.00251 (12480) covalent geometry : angle 0.54391 (16908) SS BOND : bond 0.00182 ( 12) SS BOND : angle 1.25345 ( 24) hydrogen bonds : bond 0.03664 ( 447) hydrogen bonds : angle 4.96746 ( 1323) link_ALPHA1-3 : bond 0.00310 ( 3) link_ALPHA1-3 : angle 1.53067 ( 9) link_BETA1-2 : bond 0.00342 ( 3) link_BETA1-2 : angle 0.83773 ( 9) link_BETA1-4 : bond 0.00840 ( 9) link_BETA1-4 : angle 1.84311 ( 27) link_BETA2-3 : bond 0.00576 ( 3) link_BETA2-3 : angle 4.03280 ( 9) link_NAG-ASN : bond 0.01056 ( 15) link_NAG-ASN : angle 3.78242 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4531.21 seconds wall clock time: 78 minutes 15.21 seconds (4695.21 seconds total)