Starting phenix.real_space_refine on Fri Sep 11 18:04:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y5k_10700/09_2026/6y5k_10700.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5k_10700/09_2026/6y5k_10700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6y5k_10700/09_2026/6y5k_10700.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y5k_10700/09_2026/6y5k_10700.cif" model { file = "/net/cci-nas-00/data/ceres_data/6y5k_10700/09_2026/6y5k_10700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5k_10700/09_2026/6y5k_10700.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5k_10700/09_2026/6y5k_10700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5k_10700/09_2026/6y5k_10700.map" } resolution = 4.2 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= 0.003 sd= 0.062 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 54 5.16 5 C 6609 2.51 5 N 1854 2.21 5 O 2097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10614 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2414 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 292} Chain: "B" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1096 Classifications: {'peptide': 133} Link IDs: {'TRANS': 132} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, E, D, F Time building chain proxies: 2.02, per 1000 atoms: 0.19 Number of scatterers: 10614 At special positions: 0 Unit cell: (101.091, 98.917, 159.789, 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 54 16.00 O 2097 8.00 N 1854 7.00 C 6609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=1.75 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.46 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.00 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.79 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=1.78 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.46 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.46 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.00 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.00 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.04 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.04 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 38 " " NAG C 401 " - " ASN C 38 " " NAG E 401 " - " ASN E 38 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 413.7 milliseconds 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 36 sheets defined 32.1% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.117A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.699A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 126 Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.800A pdb=" N ILE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 4.116A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.699A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 4.116A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.700A pdb=" N GLN E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 126 Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.800A pdb=" N ILE D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 169 Processing helix chain 'F' and resid 38 through 126 Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.800A pdb=" N ILE F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 3.619A pdb=" N THR A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.964A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.519A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.703A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.494A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.184A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 27 removed outlier: 3.619A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 removed outlier: 5.965A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.519A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.703A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.495A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.925A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.184A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 24 through 27 removed outlier: 3.619A pdb=" N THR E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 52 removed outlier: 5.964A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.519A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 120 through 122 removed outlier: 6.702A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD4, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.494A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD6, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD7, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.184A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AD9, first strand: chain 'F' and resid 130 through 132 483 hydrogen bonds defined for protein. 1359 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: 1.67 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3567 1.34 - 1.46: 2442 1.46 - 1.59: 4743 1.59 - 1.71: 0 1.71 - 1.83: 72 Bond restraints: 10824 Sorted by residual: bond pdb=" N CYS A 305 " pdb=" CA CYS A 305 " ideal model delta sigma weight residual 1.455 1.492 -0.036 1.17e-02 7.31e+03 9.71e+00 bond pdb=" N CYS C 305 " pdb=" CA CYS C 305 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.17e-02 7.31e+03 9.44e+00 bond pdb=" N CYS E 305 " pdb=" CA CYS E 305 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.17e-02 7.31e+03 9.32e+00 bond pdb=" N LYS C 50 " pdb=" CA LYS C 50 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.22e+00 bond pdb=" N LYS E 50 " pdb=" CA LYS E 50 " ideal model delta sigma weight residual 1.454 1.486 -0.033 1.23e-02 6.61e+03 7.15e+00 ... (remaining 10819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 14282 2.06 - 4.12: 359 4.12 - 6.17: 35 6.17 - 8.23: 3 8.23 - 10.29: 6 Bond angle restraints: 14685 Sorted by residual: angle pdb=" C CYS C 305 " pdb=" CA CYS C 305 " pdb=" CB CYS C 305 " ideal model delta sigma weight residual 110.47 104.21 6.26 1.77e+00 3.19e-01 1.25e+01 angle pdb=" C CYS A 305 " pdb=" CA CYS A 305 " pdb=" CB CYS A 305 " ideal model delta sigma weight residual 110.47 104.21 6.26 1.77e+00 3.19e-01 1.25e+01 angle pdb=" C CYS E 305 " pdb=" CA CYS E 305 " pdb=" CB CYS E 305 " ideal model delta sigma weight residual 110.47 104.22 6.25 1.77e+00 3.19e-01 1.25e+01 angle pdb=" O CYS C 76 " pdb=" C CYS C 76 " pdb=" N ASP C 77 " ideal model delta sigma weight residual 121.99 125.98 -3.99 1.24e+00 6.50e-01 1.03e+01 angle pdb=" O CYS E 76 " pdb=" C CYS E 76 " pdb=" N ASP E 77 " ideal model delta sigma weight residual 121.99 125.97 -3.98 1.24e+00 6.50e-01 1.03e+01 ... (remaining 14680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 5927 17.15 - 34.31: 440 34.31 - 51.46: 133 51.46 - 68.61: 16 68.61 - 85.76: 12 Dihedral angle restraints: 6528 sinusoidal: 2664 harmonic: 3864 Sorted by residual: dihedral pdb=" CB CYS E 14 " pdb=" SG CYS E 14 " pdb=" SG CYS F 137 " pdb=" CB CYS F 137 " ideal model delta sinusoidal sigma weight residual -86.00 -159.46 73.46 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS C 14 " pdb=" SG CYS C 14 " pdb=" SG CYS D 137 " pdb=" CB CYS D 137 " ideal model delta sinusoidal sigma weight residual -86.00 -158.92 72.92 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS A 14 " pdb=" SG CYS A 14 " pdb=" SG CYS B 137 " pdb=" CB CYS B 137 " ideal model delta sinusoidal sigma weight residual -86.00 -158.43 72.43 1 1.00e+01 1.00e-02 6.70e+01 ... (remaining 6525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1252 0.050 - 0.100: 291 0.100 - 0.150: 80 0.150 - 0.200: 23 0.200 - 0.250: 4 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CA CYS A 305 " pdb=" N CYS A 305 " pdb=" C CYS A 305 " pdb=" CB CYS A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA CYS E 305 " pdb=" N CYS E 305 " pdb=" C CYS E 305 " pdb=" CB CYS E 305 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA CYS C 305 " pdb=" N CYS C 305 " pdb=" C CYS C 305 " pdb=" CB CYS C 305 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1647 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 190 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C GLU A 190 " -0.048 2.00e-02 2.50e+03 pdb=" O GLU A 190 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN A 191 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 190 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C GLU E 190 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU E 190 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN E 191 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 190 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C GLU C 190 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU C 190 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN C 191 " 0.016 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 197 2.66 - 3.22: 9844 3.22 - 3.78: 16679 3.78 - 4.34: 22090 4.34 - 4.90: 35982 Nonbonded interactions: 84792 Sorted by model distance: nonbonded pdb=" OG1 THR C 24 " pdb=" O VAL C 36 " model vdw 2.096 3.040 nonbonded pdb=" OG1 THR A 24 " pdb=" O VAL A 36 " model vdw 2.097 3.040 nonbonded pdb=" OG1 THR E 24 " pdb=" O VAL E 36 " model vdw 2.097 3.040 nonbonded pdb=" NH1 ARG D 76 " pdb=" OE2 GLU F 74 " model vdw 2.190 3.120 nonbonded pdb=" OD1 ASP C 275 " pdb=" N THR C 276 " model vdw 2.196 3.120 ... (remaining 84787 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.280 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 9.870 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.009 0.424 10845 Z= 0.472 Angle : 0.912 30.104 14730 Z= 0.497 Chirality : 0.051 0.250 1650 Planarity : 0.004 0.043 1917 Dihedral : 12.984 85.764 3984 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -1.98 (0.20), residues: 1323 helix: 0.39 (0.23), residues: 408 sheet: -0.52 (0.31), residues: 267 loop : -2.93 (0.17), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 255 TYR 0.012 0.002 TYR C 178 PHE 0.007 0.001 PHE A 79 TRP 0.012 0.001 TRP A 222 HIS 0.002 0.001 HIS E 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.23 (10824) covalent geometry : angle 0.75841 / 0.44 (14685) SS BOND : bond 0.20298 / 11.16 ( 18) SS BOND : angle 10.22057 / 5.30 ( 36) hydrogen bonds : bond 0.11396 / 7.43 ( 483) hydrogen bonds : angle 4.76415 / 3.24 ( 1359) link_NAG-ASN : bond 0.00085 / 0.04 ( 3) link_NAG-ASN : angle 1.96379 / 1.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 TYR cc_start: 0.8238 (m-80) cc_final: 0.7729 (m-80) REVERT: B 58 LYS cc_start: 0.9360 (mtmt) cc_final: 0.9087 (mttm) REVERT: B 61 GLU cc_start: 0.8922 (pp20) cc_final: 0.8556 (pp20) REVERT: B 64 HIS cc_start: 0.8925 (m-70) cc_final: 0.8625 (m-70) REVERT: B 86 ASP cc_start: 0.8259 (t0) cc_final: 0.7850 (t0) REVERT: C 98 TYR cc_start: 0.8956 (t80) cc_final: 0.8244 (t80) REVERT: C 137 ASN cc_start: 0.9480 (m-40) cc_final: 0.9038 (p0) REVERT: E 50 LYS cc_start: 0.8581 (mttt) cc_final: 0.8120 (tptm) REVERT: E 87 PHE cc_start: 0.7100 (t80) cc_final: 0.6661 (t80) REVERT: E 98 TYR cc_start: 0.8297 (t80) cc_final: 0.7880 (t80) REVERT: E 233 TYR cc_start: 0.7983 (m-80) cc_final: 0.7715 (m-80) REVERT: D 39 LYS cc_start: 0.9733 (mptt) cc_final: 0.9515 (mmtm) REVERT: D 58 LYS cc_start: 0.9461 (mtmt) cc_final: 0.9089 (ptpp) REVERT: D 62 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8602 (mmtt) REVERT: D 64 HIS cc_start: 0.8922 (m-70) cc_final: 0.8519 (m90) REVERT: D 86 ASP cc_start: 0.8450 (t0) cc_final: 0.8010 (t0) REVERT: D 108 ILE cc_start: 0.9723 (mt) cc_final: 0.9434 (tt) REVERT: F 38 LEU cc_start: 0.9521 (pt) cc_final: 0.9318 (pt) REVERT: F 39 LYS cc_start: 0.9736 (mptt) cc_final: 0.9515 (mmtm) REVERT: F 58 LYS cc_start: 0.9404 (mtmt) cc_final: 0.9203 (ptpp) REVERT: F 59 THR cc_start: 0.9595 (p) cc_final: 0.8947 (p) REVERT: F 63 PHE cc_start: 0.9340 (m-10) cc_final: 0.9049 (m-80) REVERT: F 64 HIS cc_start: 0.8930 (m-70) cc_final: 0.8560 (m90) REVERT: F 66 ILE cc_start: 0.9704 (mt) cc_final: 0.9415 (mt) REVERT: F 70 PHE cc_start: 0.8781 (m-80) cc_final: 0.8216 (m-80) REVERT: F 78 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8499 (mm-40) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1342 time to fit residues: 48.4024 Evaluate side-chains 160 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 ASN A 184 HIS A 197 GLN A 216 ASN A 285 ASN A 298 ASN B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS C 173 ASN C 184 HIS C 197 GLN C 216 ASN C 285 ASN C 298 ASN E 173 ASN E 184 HIS E 197 GLN E 216 ASN E 285 ASN E 298 ASN D 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS F 104 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.087239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.059063 restraints weight = 46368.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.057914 restraints weight = 26684.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.058498 restraints weight = 20436.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.058979 restraints weight = 17696.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.059267 restraints weight = 15788.778| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10845 Z= 0.114 Angle : 0.553 7.294 14730 Z= 0.294 Chirality : 0.043 0.145 1650 Planarity : 0.004 0.044 1917 Dihedral : 4.336 34.332 1443 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.72 (0.21), residues: 1323 helix: 1.59 (0.24), residues: 399 sheet: 0.19 (0.35), residues: 240 loop : -2.13 (0.18), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 123 TYR 0.012 0.001 TYR E 100 PHE 0.030 0.002 PHE B 70 TRP 0.024 0.002 TRP C 180 HIS 0.008 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10824) covalent geometry : angle 0.54924 / 0.29 (14685) SS BOND : bond 0.00274 / 0.17 ( 18) SS BOND : angle 1.47860 / 1.16 ( 36) hydrogen bonds : bond 0.03172 / 2.19 ( 483) hydrogen bonds : angle 4.04071 / 2.80 ( 1359) link_NAG-ASN : bond 0.00278 / 0.14 ( 3) link_NAG-ASN : angle 0.60968 / 0.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.8741 (m-80) cc_final: 0.8464 (m-80) REVERT: A 137 ASN cc_start: 0.9459 (m-40) cc_final: 0.8699 (p0) REVERT: A 233 TYR cc_start: 0.7971 (m-80) cc_final: 0.7711 (m-80) REVERT: B 54 ARG cc_start: 0.9332 (mtp85) cc_final: 0.8670 (ptm-80) REVERT: B 58 LYS cc_start: 0.9377 (mtmt) cc_final: 0.9087 (mttm) REVERT: B 64 HIS cc_start: 0.8850 (m-70) cc_final: 0.8609 (m-70) REVERT: B 86 ASP cc_start: 0.8670 (t0) cc_final: 0.8099 (t0) REVERT: B 133 MET cc_start: 0.7644 (ptt) cc_final: 0.7178 (ppp) REVERT: C 70 LEU cc_start: 0.7907 (tp) cc_final: 0.7534 (mt) REVERT: C 98 TYR cc_start: 0.8845 (t80) cc_final: 0.8154 (t80) REVERT: C 137 ASN cc_start: 0.9462 (m-40) cc_final: 0.8861 (p0) REVERT: C 184 HIS cc_start: 0.7966 (m-70) cc_final: 0.7532 (m90) REVERT: C 233 TYR cc_start: 0.7867 (m-80) cc_final: 0.7618 (m-80) REVERT: E 50 LYS cc_start: 0.8452 (mttt) cc_final: 0.8019 (tptm) REVERT: E 70 LEU cc_start: 0.8010 (tp) cc_final: 0.7776 (mt) REVERT: E 87 PHE cc_start: 0.6396 (t80) cc_final: 0.5711 (t80) REVERT: E 98 TYR cc_start: 0.8377 (t80) cc_final: 0.7927 (t80) REVERT: D 58 LYS cc_start: 0.9424 (mtmt) cc_final: 0.9077 (ptpp) REVERT: D 62 LYS cc_start: 0.9085 (mmtt) cc_final: 0.8866 (mmtt) REVERT: D 64 HIS cc_start: 0.8885 (m-70) cc_final: 0.8484 (m-70) REVERT: D 86 ASP cc_start: 0.8633 (t0) cc_final: 0.8081 (t0) REVERT: D 90 ASP cc_start: 0.9033 (m-30) cc_final: 0.8787 (m-30) REVERT: D 108 ILE cc_start: 0.9701 (mt) cc_final: 0.9499 (tt) REVERT: F 59 THR cc_start: 0.9521 (p) cc_final: 0.8714 (p) REVERT: F 63 PHE cc_start: 0.9272 (m-10) cc_final: 0.8908 (m-80) REVERT: F 66 ILE cc_start: 0.9595 (mt) cc_final: 0.9334 (mt) REVERT: F 70 PHE cc_start: 0.8785 (m-80) cc_final: 0.8239 (m-80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1337 time to fit residues: 38.3677 Evaluate side-chains 143 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 56 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 184 HIS B 64 HIS B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS E 75 HIS E 184 HIS E 298 ASN D 64 HIS D 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN F 64 HIS F 104 ASN F 146 ASN F 159 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.089130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.061892 restraints weight = 52562.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.059945 restraints weight = 29649.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.060547 restraints weight = 25810.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.060624 restraints weight = 22303.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.060725 restraints weight = 21041.058| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10845 Z= 0.201 Angle : 0.611 7.344 14730 Z= 0.327 Chirality : 0.045 0.177 1650 Planarity : 0.004 0.060 1917 Dihedral : 4.536 34.026 1443 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.08 % Allowed : 4.04 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.37 (0.21), residues: 1323 helix: 1.64 (0.24), residues: 399 sheet: 0.25 (0.33), residues: 255 loop : -1.72 (0.20), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 124 TYR 0.023 0.002 TYR B 83 PHE 0.015 0.002 PHE D 70 TRP 0.022 0.002 TRP A 127 HIS 0.008 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (10824) covalent geometry : angle 0.60426 / 0.32 (14685) SS BOND : bond 0.00394 / 0.26 ( 18) SS BOND : angle 1.81517 / 1.19 ( 36) hydrogen bonds : bond 0.03481 / 2.42 ( 483) hydrogen bonds : angle 4.41516 / 3.05 ( 1359) link_NAG-ASN : bond 0.00283 / 0.14 ( 3) link_NAG-ASN : angle 1.16011 / 0.53 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9406 (m-40) cc_final: 0.8581 (p0) REVERT: B 54 ARG cc_start: 0.9030 (mtp85) cc_final: 0.8714 (ptm-80) REVERT: B 64 HIS cc_start: 0.8662 (m170) cc_final: 0.8219 (m-70) REVERT: B 86 ASP cc_start: 0.8388 (t0) cc_final: 0.7899 (t0) REVERT: B 118 LEU cc_start: 0.9681 (pp) cc_final: 0.9405 (pp) REVERT: B 133 MET cc_start: 0.7761 (ptt) cc_final: 0.7239 (ppp) REVERT: C 70 LEU cc_start: 0.7850 (tp) cc_final: 0.7380 (mt) REVERT: C 98 TYR cc_start: 0.8866 (t80) cc_final: 0.8378 (t80) REVERT: C 233 TYR cc_start: 0.8217 (m-80) cc_final: 0.7718 (m-80) REVERT: E 50 LYS cc_start: 0.8714 (mttt) cc_final: 0.8260 (tptm) REVERT: E 98 TYR cc_start: 0.8619 (t80) cc_final: 0.8145 (t80) REVERT: D 42 GLN cc_start: 0.9511 (mt0) cc_final: 0.9249 (mt0) REVERT: D 54 ARG cc_start: 0.9099 (mtp85) cc_final: 0.8554 (ptm-80) REVERT: D 58 LYS cc_start: 0.9328 (mtmt) cc_final: 0.8790 (mttm) REVERT: D 62 LYS cc_start: 0.9206 (mmtt) cc_final: 0.8970 (mmtt) REVERT: D 86 ASP cc_start: 0.8348 (t0) cc_final: 0.7878 (t0) REVERT: D 108 ILE cc_start: 0.9682 (mt) cc_final: 0.9476 (tt) REVERT: F 59 THR cc_start: 0.9358 (p) cc_final: 0.8431 (p) REVERT: F 62 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8695 (mmmm) REVERT: F 63 PHE cc_start: 0.9109 (m-10) cc_final: 0.8679 (m-80) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1281 time to fit residues: 32.1893 Evaluate side-chains 132 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 22 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 90 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS E 184 HIS D 64 HIS D 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.089798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.063122 restraints weight = 52236.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.061432 restraints weight = 28766.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.061663 restraints weight = 28129.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062082 restraints weight = 22091.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062154 restraints weight = 20549.513| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10845 Z= 0.131 Angle : 0.552 7.043 14730 Z= 0.291 Chirality : 0.044 0.153 1650 Planarity : 0.004 0.035 1917 Dihedral : 4.291 34.387 1443 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.25 % Allowed : 2.19 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.22 (0.22), residues: 1323 helix: 1.93 (0.24), residues: 402 sheet: 0.15 (0.34), residues: 240 loop : -1.63 (0.20), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 163 TYR 0.010 0.001 TYR B 83 PHE 0.012 0.001 PHE F 70 TRP 0.019 0.002 TRP C 127 HIS 0.016 0.001 HIS D 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10824) covalent geometry : angle 0.54641 / 0.29 (14685) SS BOND : bond 0.00512 / 0.33 ( 18) SS BOND : angle 1.67862 / 1.06 ( 36) hydrogen bonds : bond 0.03129 / 2.18 ( 483) hydrogen bonds : angle 4.19876 / 2.93 ( 1359) link_NAG-ASN : bond 0.00229 / 0.11 ( 3) link_NAG-ASN : angle 0.88139 / 0.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9338 (m-40) cc_final: 0.8440 (p0) REVERT: A 233 TYR cc_start: 0.8360 (m-80) cc_final: 0.8134 (m-80) REVERT: B 54 ARG cc_start: 0.9048 (mtp85) cc_final: 0.8748 (ptm-80) REVERT: B 64 HIS cc_start: 0.8596 (m170) cc_final: 0.8209 (m90) REVERT: B 86 ASP cc_start: 0.8458 (t0) cc_final: 0.7898 (t0) REVERT: B 133 MET cc_start: 0.7753 (ptt) cc_final: 0.7218 (ppp) REVERT: C 70 LEU cc_start: 0.7857 (tp) cc_final: 0.7140 (pp) REVERT: C 98 TYR cc_start: 0.8855 (t80) cc_final: 0.8359 (t80) REVERT: C 100 TYR cc_start: 0.7173 (p90) cc_final: 0.6944 (p90) REVERT: C 137 ASN cc_start: 0.9329 (m-40) cc_final: 0.8737 (p0) REVERT: C 233 TYR cc_start: 0.8125 (m-80) cc_final: 0.7641 (m-80) REVERT: E 50 LYS cc_start: 0.8732 (mttt) cc_final: 0.8318 (tptm) REVERT: E 98 TYR cc_start: 0.7104 (t80) cc_final: 0.6548 (t80) REVERT: E 100 TYR cc_start: 0.5078 (p90) cc_final: 0.4843 (p90) REVERT: D 39 LYS cc_start: 0.9712 (mmtm) cc_final: 0.9394 (mmmt) REVERT: D 42 GLN cc_start: 0.9485 (mt0) cc_final: 0.9071 (mt0) REVERT: D 54 ARG cc_start: 0.9115 (mtp85) cc_final: 0.8553 (ptm-80) REVERT: D 58 LYS cc_start: 0.9371 (mtmt) cc_final: 0.8854 (mttm) REVERT: D 61 GLU cc_start: 0.8716 (pp20) cc_final: 0.8437 (pp20) REVERT: D 86 ASP cc_start: 0.8361 (t0) cc_final: 0.7838 (t0) REVERT: D 90 ASP cc_start: 0.8732 (m-30) cc_final: 0.8507 (m-30) REVERT: F 59 THR cc_start: 0.9373 (p) cc_final: 0.8457 (p) REVERT: F 61 GLU cc_start: 0.8695 (pp20) cc_final: 0.7777 (pp20) REVERT: F 62 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8708 (mmtt) REVERT: F 63 PHE cc_start: 0.9097 (m-10) cc_final: 0.8825 (m-80) REVERT: F 66 ILE cc_start: 0.9585 (mt) cc_final: 0.9159 (mt) REVERT: F 70 PHE cc_start: 0.8469 (m-80) cc_final: 0.8036 (m-80) REVERT: F 86 ASP cc_start: 0.8386 (t0) cc_final: 0.7784 (t0) outliers start: 3 outliers final: 2 residues processed: 198 average time/residue: 0.1269 time to fit residues: 33.5195 Evaluate side-chains 142 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS B 60 ASN B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN C 184 HIS E 184 HIS E 298 ASN D 53 ASN D 60 ASN D 104 ASN F 53 ASN F 60 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.080104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.048423 restraints weight = 48525.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.050850 restraints weight = 24264.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.052214 restraints weight = 16245.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.052828 restraints weight = 13104.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.053226 restraints weight = 11844.923| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 10845 Z= 0.302 Angle : 0.729 9.504 14730 Z= 0.387 Chirality : 0.048 0.217 1650 Planarity : 0.005 0.052 1917 Dihedral : 5.008 34.055 1443 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.96 (0.21), residues: 1323 helix: 0.98 (0.24), residues: 408 sheet: -0.35 (0.30), residues: 258 loop : -1.87 (0.20), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 163 TYR 0.024 0.002 TYR F 83 PHE 0.015 0.002 PHE C 120 TRP 0.022 0.002 TRP C 127 HIS 0.007 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.30 (10824) covalent geometry : angle 0.71843 / 0.38 (14685) SS BOND : bond 0.00927 / 0.61 ( 18) SS BOND : angle 2.46723 / 1.58 ( 36) hydrogen bonds : bond 0.04176 / 2.88 ( 483) hydrogen bonds : angle 5.02408 / 3.46 ( 1359) link_NAG-ASN : bond 0.00433 / 0.22 ( 3) link_NAG-ASN : angle 1.88067 / 0.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 SER cc_start: 0.8679 (t) cc_final: 0.8431 (t) REVERT: A 233 TYR cc_start: 0.8492 (m-80) cc_final: 0.8094 (m-80) REVERT: B 62 LYS cc_start: 0.9281 (mmtt) cc_final: 0.8937 (mmtt) REVERT: B 64 HIS cc_start: 0.9013 (m170) cc_final: 0.8402 (m90) REVERT: B 68 LYS cc_start: 0.9480 (mmtm) cc_final: 0.9190 (mmtm) REVERT: B 86 ASP cc_start: 0.8478 (t0) cc_final: 0.8022 (t0) REVERT: B 90 ASP cc_start: 0.8825 (m-30) cc_final: 0.8586 (m-30) REVERT: B 114 GLU cc_start: 0.9444 (tp30) cc_final: 0.9166 (tp30) REVERT: B 118 LEU cc_start: 0.9667 (pp) cc_final: 0.9371 (pp) REVERT: B 133 MET cc_start: 0.7863 (ptt) cc_final: 0.7326 (ppp) REVERT: C 70 LEU cc_start: 0.7601 (tp) cc_final: 0.7164 (mt) REVERT: C 98 TYR cc_start: 0.8939 (t80) cc_final: 0.8423 (t80) REVERT: C 137 ASN cc_start: 0.9408 (m-40) cc_final: 0.8874 (p0) REVERT: C 231 SER cc_start: 0.8693 (m) cc_final: 0.8070 (m) REVERT: C 233 TYR cc_start: 0.8395 (m-80) cc_final: 0.7971 (m-80) REVERT: C 260 MET cc_start: 0.6979 (ppp) cc_final: 0.6529 (mpp) REVERT: C 261 ARG cc_start: 0.4701 (mtt90) cc_final: 0.3299 (ptt90) REVERT: E 50 LYS cc_start: 0.8821 (mttt) cc_final: 0.8216 (mmmt) REVERT: E 98 TYR cc_start: 0.7649 (t80) cc_final: 0.7139 (t80) REVERT: E 233 TYR cc_start: 0.8282 (m-80) cc_final: 0.8060 (m-80) REVERT: D 51 LYS cc_start: 0.9669 (mmtt) cc_final: 0.9124 (mmtp) REVERT: D 54 ARG cc_start: 0.9380 (mtp85) cc_final: 0.9092 (mtm110) REVERT: D 67 GLU cc_start: 0.9376 (pt0) cc_final: 0.8754 (pp20) REVERT: D 86 ASP cc_start: 0.8472 (t0) cc_final: 0.8040 (t0) REVERT: D 90 ASP cc_start: 0.8586 (m-30) cc_final: 0.8356 (m-30) REVERT: F 59 THR cc_start: 0.9596 (p) cc_final: 0.8773 (p) REVERT: F 63 PHE cc_start: 0.9481 (m-10) cc_final: 0.9095 (m-80) REVERT: F 133 MET cc_start: 0.7885 (ptt) cc_final: 0.7444 (ptt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1245 time to fit residues: 29.0437 Evaluate side-chains 134 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 GLN B 104 ASN B 105 GLN C 184 HIS D 78 GLN D 104 ASN F 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.088503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.061854 restraints weight = 52306.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.059352 restraints weight = 35360.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.059850 restraints weight = 31011.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.060248 restraints weight = 23818.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.060336 restraints weight = 21716.362| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10845 Z= 0.133 Angle : 0.581 11.586 14730 Z= 0.300 Chirality : 0.044 0.161 1650 Planarity : 0.004 0.036 1917 Dihedral : 4.408 35.043 1443 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.46 (0.21), residues: 1323 helix: 1.53 (0.24), residues: 408 sheet: -0.01 (0.33), residues: 228 loop : -1.62 (0.20), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 163 TYR 0.009 0.001 TYR F 83 PHE 0.011 0.001 PHE C 120 TRP 0.020 0.001 TRP C 127 HIS 0.009 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10824) covalent geometry : angle 0.57433 / 0.30 (14685) SS BOND : bond 0.00582 / 0.38 ( 18) SS BOND : angle 1.83784 / 0.98 ( 36) hydrogen bonds : bond 0.03099 / 2.14 ( 483) hydrogen bonds : angle 4.30702 / 3.00 ( 1359) link_NAG-ASN : bond 0.00290 / 0.14 ( 3) link_NAG-ASN : angle 1.22563 / 0.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9358 (m-40) cc_final: 0.8623 (p0) REVERT: A 231 SER cc_start: 0.8604 (t) cc_final: 0.8317 (t) REVERT: A 233 TYR cc_start: 0.8195 (m-80) cc_final: 0.7919 (m-80) REVERT: A 280 GLU cc_start: 0.8916 (mp0) cc_final: 0.8355 (pm20) REVERT: A 288 ILE cc_start: 0.8939 (mt) cc_final: 0.8449 (mt) REVERT: B 62 LYS cc_start: 0.9223 (mmtt) cc_final: 0.8873 (mttp) REVERT: B 64 HIS cc_start: 0.8729 (m170) cc_final: 0.8155 (m90) REVERT: B 68 LYS cc_start: 0.9398 (mmtm) cc_final: 0.9125 (mmtm) REVERT: B 86 ASP cc_start: 0.8560 (t0) cc_final: 0.8061 (t0) REVERT: B 118 LEU cc_start: 0.9695 (pp) cc_final: 0.9383 (pp) REVERT: B 133 MET cc_start: 0.7878 (ptt) cc_final: 0.7452 (ppp) REVERT: C 70 LEU cc_start: 0.7565 (tp) cc_final: 0.7259 (mt) REVERT: C 98 TYR cc_start: 0.8978 (t80) cc_final: 0.8437 (t80) REVERT: C 137 ASN cc_start: 0.9423 (m-40) cc_final: 0.8835 (p0) REVERT: C 231 SER cc_start: 0.8461 (m) cc_final: 0.7869 (m) REVERT: C 233 TYR cc_start: 0.8245 (m-80) cc_final: 0.7878 (m-80) REVERT: C 260 MET cc_start: 0.7133 (ppp) cc_final: 0.6653 (mpp) REVERT: C 261 ARG cc_start: 0.5068 (mtt90) cc_final: 0.3472 (ptt90) REVERT: E 50 LYS cc_start: 0.8743 (mttt) cc_final: 0.8275 (tptm) REVERT: D 39 LYS cc_start: 0.9733 (mmtm) cc_final: 0.9463 (mmmt) REVERT: D 42 GLN cc_start: 0.9468 (mt0) cc_final: 0.8991 (mt0) REVERT: D 54 ARG cc_start: 0.9116 (mtp85) cc_final: 0.8588 (ptm-80) REVERT: D 58 LYS cc_start: 0.9422 (mtmt) cc_final: 0.8957 (mttm) REVERT: D 86 ASP cc_start: 0.8452 (t0) cc_final: 0.7990 (t0) REVERT: D 90 ASP cc_start: 0.8754 (m-30) cc_final: 0.8491 (m-30) REVERT: D 133 MET cc_start: 0.7937 (ptt) cc_final: 0.7457 (mpp) REVERT: F 38 LEU cc_start: 0.9459 (pt) cc_final: 0.9247 (pt) REVERT: F 39 LYS cc_start: 0.9722 (mmtm) cc_final: 0.9486 (mmmt) REVERT: F 59 THR cc_start: 0.9423 (p) cc_final: 0.8435 (p) REVERT: F 63 PHE cc_start: 0.9200 (m-10) cc_final: 0.8845 (m-80) REVERT: F 66 ILE cc_start: 0.9637 (mt) cc_final: 0.9183 (mt) REVERT: F 70 PHE cc_start: 0.8582 (m-80) cc_final: 0.8148 (m-80) REVERT: F 86 ASP cc_start: 0.8457 (t0) cc_final: 0.7792 (t0) REVERT: F 90 ASP cc_start: 0.9022 (m-30) cc_final: 0.8659 (m-30) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1191 time to fit residues: 28.7773 Evaluate side-chains 146 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 51 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 125 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.079702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.048273 restraints weight = 48751.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.050668 restraints weight = 24362.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.051989 restraints weight = 16315.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.052725 restraints weight = 13171.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.053025 restraints weight = 11806.217| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 10845 Z= 0.295 Angle : 0.727 9.684 14730 Z= 0.386 Chirality : 0.048 0.205 1650 Planarity : 0.005 0.037 1917 Dihedral : 5.143 50.080 1443 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.02 (0.21), residues: 1323 helix: 1.11 (0.24), residues: 402 sheet: -0.69 (0.30), residues: 252 loop : -1.85 (0.20), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 123 TYR 0.018 0.002 TYR B 83 PHE 0.013 0.002 PHE C 120 TRP 0.019 0.002 TRP C 127 HIS 0.012 0.002 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.29 (10824) covalent geometry : angle 0.71776 / 0.38 (14685) SS BOND : bond 0.01038 / 0.64 ( 18) SS BOND : angle 2.22900 / 1.37 ( 36) hydrogen bonds : bond 0.04146 / 2.89 ( 483) hydrogen bonds : angle 4.99864 / 3.45 ( 1359) link_NAG-ASN : bond 0.00434 / 0.22 ( 3) link_NAG-ASN : angle 1.85697 / 0.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 TYR cc_start: 0.8309 (m-80) cc_final: 0.7989 (m-80) REVERT: B 62 LYS cc_start: 0.9335 (mmtt) cc_final: 0.9066 (mttm) REVERT: B 64 HIS cc_start: 0.9002 (m170) cc_final: 0.8525 (m90) REVERT: B 69 GLU cc_start: 0.9113 (mp0) cc_final: 0.8868 (mp0) REVERT: B 86 ASP cc_start: 0.8523 (t0) cc_final: 0.8196 (t0) REVERT: B 114 GLU cc_start: 0.9401 (tm-30) cc_final: 0.9102 (tm-30) REVERT: B 133 MET cc_start: 0.7768 (ptt) cc_final: 0.7339 (ppp) REVERT: C 70 LEU cc_start: 0.7610 (tp) cc_final: 0.7103 (mt) REVERT: C 98 TYR cc_start: 0.8969 (t80) cc_final: 0.8493 (t80) REVERT: C 137 ASN cc_start: 0.9362 (m-40) cc_final: 0.8849 (p0) REVERT: C 231 SER cc_start: 0.8631 (m) cc_final: 0.8061 (m) REVERT: C 233 TYR cc_start: 0.8405 (m-80) cc_final: 0.8038 (m-80) REVERT: E 50 LYS cc_start: 0.8829 (mttt) cc_final: 0.8320 (tptp) REVERT: D 58 LYS cc_start: 0.9522 (mtmt) cc_final: 0.9316 (mttm) REVERT: D 67 GLU cc_start: 0.9369 (pt0) cc_final: 0.8766 (pp20) REVERT: D 86 ASP cc_start: 0.8485 (t0) cc_final: 0.8042 (t0) REVERT: D 90 ASP cc_start: 0.8585 (m-30) cc_final: 0.8356 (m-30) REVERT: D 114 GLU cc_start: 0.9164 (pp20) cc_final: 0.8960 (pp20) REVERT: D 133 MET cc_start: 0.7908 (ptt) cc_final: 0.7545 (mpp) REVERT: F 59 THR cc_start: 0.9596 (p) cc_final: 0.8874 (p) REVERT: F 62 LYS cc_start: 0.9400 (mmtt) cc_final: 0.9073 (mttp) REVERT: F 63 PHE cc_start: 0.9390 (m-10) cc_final: 0.9020 (m-80) REVERT: F 66 ILE cc_start: 0.9703 (mt) cc_final: 0.9301 (mt) REVERT: F 70 PHE cc_start: 0.8861 (m-80) cc_final: 0.8335 (m-80) REVERT: F 133 MET cc_start: 0.7852 (ptt) cc_final: 0.7467 (ptt) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1171 time to fit residues: 27.3522 Evaluate side-chains 138 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 ASN B 60 ASN B 104 ASN D 104 ASN D 125 GLN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.088207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.061441 restraints weight = 51756.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.059557 restraints weight = 28895.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.060079 restraints weight = 25890.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.060165 restraints weight = 22284.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.060235 restraints weight = 21075.115| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10845 Z= 0.121 Angle : 0.606 9.694 14730 Z= 0.317 Chirality : 0.045 0.223 1650 Planarity : 0.004 0.039 1917 Dihedral : 4.478 35.190 1443 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -0.54 (0.22), residues: 1323 helix: 1.58 (0.25), residues: 408 sheet: -0.26 (0.32), residues: 246 loop : -1.69 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 127 TYR 0.009 0.001 TYR E 98 PHE 0.008 0.001 PHE D 70 TRP 0.015 0.001 TRP C 153 HIS 0.009 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10824) covalent geometry : angle 0.59564 / 0.31 (14685) SS BOND : bond 0.00691 / 0.39 ( 18) SS BOND : angle 2.21730 / 1.18 ( 36) hydrogen bonds : bond 0.03088 / 2.14 ( 483) hydrogen bonds : angle 4.41845 / 3.08 ( 1359) link_NAG-ASN : bond 0.00227 / 0.11 ( 3) link_NAG-ASN : angle 1.33385 / 0.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8796 (mttt) cc_final: 0.8383 (ttmt) REVERT: A 98 TYR cc_start: 0.8115 (t80) cc_final: 0.7708 (t80) REVERT: A 137 ASN cc_start: 0.9297 (m-40) cc_final: 0.8503 (p0) REVERT: A 177 LEU cc_start: 0.8955 (mm) cc_final: 0.8579 (mm) REVERT: A 260 MET cc_start: 0.7103 (ppp) cc_final: 0.6777 (ptm) REVERT: A 280 GLU cc_start: 0.8945 (mp0) cc_final: 0.8385 (pm20) REVERT: A 288 ILE cc_start: 0.8921 (mt) cc_final: 0.8586 (mt) REVERT: B 64 HIS cc_start: 0.8641 (m170) cc_final: 0.8155 (m90) REVERT: B 68 LYS cc_start: 0.9372 (mmtm) cc_final: 0.9116 (mmtm) REVERT: B 69 GLU cc_start: 0.8824 (mp0) cc_final: 0.8586 (mp0) REVERT: B 86 ASP cc_start: 0.8433 (t0) cc_final: 0.7890 (t0) REVERT: B 90 ASP cc_start: 0.8929 (m-30) cc_final: 0.8701 (m-30) REVERT: B 133 MET cc_start: 0.7812 (ptt) cc_final: 0.7440 (ppp) REVERT: C 70 LEU cc_start: 0.7565 (tp) cc_final: 0.7269 (mt) REVERT: C 98 TYR cc_start: 0.8968 (t80) cc_final: 0.8445 (t80) REVERT: C 137 ASN cc_start: 0.9327 (m-40) cc_final: 0.8760 (p0) REVERT: C 231 SER cc_start: 0.8440 (m) cc_final: 0.7738 (m) REVERT: C 233 TYR cc_start: 0.8292 (m-80) cc_final: 0.7972 (m-80) REVERT: C 260 MET cc_start: 0.7493 (ppp) cc_final: 0.6907 (ptp) REVERT: C 261 ARG cc_start: 0.4752 (mtt90) cc_final: 0.3177 (ppt170) REVERT: C 320 MET cc_start: 0.5759 (ptm) cc_final: 0.5454 (ptm) REVERT: E 50 LYS cc_start: 0.8760 (mttt) cc_final: 0.8304 (tptm) REVERT: D 39 LYS cc_start: 0.9722 (mmtm) cc_final: 0.9469 (mmmt) REVERT: D 42 GLN cc_start: 0.9416 (mt0) cc_final: 0.8970 (mt0) REVERT: D 59 THR cc_start: 0.9341 (p) cc_final: 0.8630 (p) REVERT: D 62 LYS cc_start: 0.9435 (mmtt) cc_final: 0.9116 (mmmt) REVERT: D 63 PHE cc_start: 0.9134 (m-10) cc_final: 0.8872 (m-80) REVERT: D 64 HIS cc_start: 0.8726 (m170) cc_final: 0.8244 (m90) REVERT: D 86 ASP cc_start: 0.8318 (t0) cc_final: 0.7840 (t0) REVERT: D 90 ASP cc_start: 0.8717 (m-30) cc_final: 0.8436 (m-30) REVERT: D 124 ARG cc_start: 0.9513 (mtm-85) cc_final: 0.9272 (mtt180) REVERT: D 126 LEU cc_start: 0.9504 (pp) cc_final: 0.8923 (pp) REVERT: D 133 MET cc_start: 0.7965 (ptt) cc_final: 0.7605 (mpp) REVERT: F 42 GLN cc_start: 0.9378 (mt0) cc_final: 0.8988 (mt0) REVERT: F 59 THR cc_start: 0.9362 (p) cc_final: 0.8371 (p) REVERT: F 63 PHE cc_start: 0.9050 (m-10) cc_final: 0.8837 (m-80) REVERT: F 65 GLN cc_start: 0.9118 (pm20) cc_final: 0.8693 (pm20) REVERT: F 66 ILE cc_start: 0.9617 (mt) cc_final: 0.9160 (mt) REVERT: F 70 PHE cc_start: 0.8499 (m-80) cc_final: 0.8044 (m-80) REVERT: F 86 ASP cc_start: 0.8304 (t0) cc_final: 0.7666 (t0) REVERT: F 90 ASP cc_start: 0.8957 (m-30) cc_final: 0.8586 (m-30) REVERT: F 133 MET cc_start: 0.7902 (ptt) cc_final: 0.7549 (mpp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1090 time to fit residues: 27.4688 Evaluate side-chains 149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 100 optimal weight: 0.0040 chunk 51 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 114 optimal weight: 0.1980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 104 ASN D 104 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.087803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.061000 restraints weight = 51421.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.058967 restraints weight = 29232.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.059535 restraints weight = 26019.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.059627 restraints weight = 22431.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.059666 restraints weight = 21053.410| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10845 Z= 0.138 Angle : 0.617 11.599 14730 Z= 0.325 Chirality : 0.045 0.175 1650 Planarity : 0.004 0.064 1917 Dihedral : 4.550 46.020 1443 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -0.53 (0.22), residues: 1323 helix: 1.56 (0.24), residues: 408 sheet: -0.24 (0.32), residues: 246 loop : -1.68 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 127 TYR 0.008 0.001 TYR F 83 PHE 0.013 0.001 PHE D 63 TRP 0.014 0.001 TRP C 153 HIS 0.009 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (10824) covalent geometry : angle 0.61191 / 0.32 (14685) SS BOND : bond 0.00520 / 0.34 ( 18) SS BOND : angle 1.58848 / 0.97 ( 36) hydrogen bonds : bond 0.03303 / 2.28 ( 483) hydrogen bonds : angle 4.40056 / 3.06 ( 1359) link_NAG-ASN : bond 0.00218 / 0.11 ( 3) link_NAG-ASN : angle 1.16386 / 0.55 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9294 (m-40) cc_final: 0.8484 (p0) REVERT: A 177 LEU cc_start: 0.8909 (mm) cc_final: 0.8567 (mm) REVERT: A 260 MET cc_start: 0.7202 (ppp) cc_final: 0.6791 (ptm) REVERT: A 280 GLU cc_start: 0.8913 (mp0) cc_final: 0.8445 (pm20) REVERT: A 288 ILE cc_start: 0.8958 (mt) cc_final: 0.8552 (mt) REVERT: B 64 HIS cc_start: 0.8735 (m170) cc_final: 0.8192 (m90) REVERT: B 66 ILE cc_start: 0.9670 (mt) cc_final: 0.9139 (mt) REVERT: B 68 LYS cc_start: 0.9400 (mmtm) cc_final: 0.9166 (mmtm) REVERT: B 70 PHE cc_start: 0.8620 (m-80) cc_final: 0.8102 (m-80) REVERT: B 86 ASP cc_start: 0.8480 (t0) cc_final: 0.7946 (t0) REVERT: B 90 ASP cc_start: 0.8963 (m-30) cc_final: 0.8703 (m-30) REVERT: B 115 MET cc_start: 0.9008 (tpt) cc_final: 0.8373 (ttt) REVERT: B 118 LEU cc_start: 0.9716 (pp) cc_final: 0.9256 (pp) REVERT: B 133 MET cc_start: 0.7871 (ptt) cc_final: 0.7506 (ppp) REVERT: C 70 LEU cc_start: 0.7574 (tp) cc_final: 0.7225 (mt) REVERT: C 98 TYR cc_start: 0.8966 (t80) cc_final: 0.8460 (t80) REVERT: C 137 ASN cc_start: 0.9331 (m-40) cc_final: 0.8755 (p0) REVERT: C 231 SER cc_start: 0.8437 (m) cc_final: 0.7766 (m) REVERT: C 233 TYR cc_start: 0.8293 (m-80) cc_final: 0.7981 (m-80) REVERT: C 260 MET cc_start: 0.7499 (ppp) cc_final: 0.6988 (ptp) REVERT: C 261 ARG cc_start: 0.4768 (mtt90) cc_final: 0.3079 (ppt170) REVERT: C 320 MET cc_start: 0.5702 (ptm) cc_final: 0.5492 (ptm) REVERT: E 50 LYS cc_start: 0.8746 (mttt) cc_final: 0.8177 (mmmt) REVERT: E 260 MET cc_start: 0.7091 (ptp) cc_final: 0.6821 (pmm) REVERT: D 39 LYS cc_start: 0.9724 (mmtm) cc_final: 0.9474 (mmmt) REVERT: D 42 GLN cc_start: 0.9435 (mt0) cc_final: 0.8987 (mt0) REVERT: D 59 THR cc_start: 0.9322 (p) cc_final: 0.8646 (p) REVERT: D 63 PHE cc_start: 0.9083 (m-10) cc_final: 0.8830 (m-80) REVERT: D 64 HIS cc_start: 0.8782 (m170) cc_final: 0.8358 (m90) REVERT: D 69 GLU cc_start: 0.8913 (mp0) cc_final: 0.8706 (mp0) REVERT: D 86 ASP cc_start: 0.8410 (t0) cc_final: 0.7916 (t0) REVERT: D 90 ASP cc_start: 0.8763 (m-30) cc_final: 0.8476 (m-30) REVERT: D 133 MET cc_start: 0.8017 (ptt) cc_final: 0.7677 (mpp) REVERT: F 42 GLN cc_start: 0.9433 (mt0) cc_final: 0.9044 (mt0) REVERT: F 59 THR cc_start: 0.9420 (p) cc_final: 0.8443 (p) REVERT: F 63 PHE cc_start: 0.9071 (m-10) cc_final: 0.8759 (m-80) REVERT: F 66 ILE cc_start: 0.9577 (mt) cc_final: 0.9217 (mt) REVERT: F 68 LYS cc_start: 0.9451 (ptmt) cc_final: 0.9061 (pttp) REVERT: F 70 PHE cc_start: 0.8545 (m-80) cc_final: 0.8138 (m-80) REVERT: F 86 ASP cc_start: 0.8365 (t0) cc_final: 0.7725 (t0) REVERT: F 90 ASP cc_start: 0.8996 (m-30) cc_final: 0.8636 (m-30) REVERT: F 121 LYS cc_start: 0.9743 (ptpp) cc_final: 0.9390 (ptpp) REVERT: F 133 MET cc_start: 0.7948 (ptt) cc_final: 0.7653 (mpp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1144 time to fit residues: 28.5979 Evaluate side-chains 141 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.088214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.061698 restraints weight = 51563.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.059539 restraints weight = 28148.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.060168 restraints weight = 25901.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.060406 restraints weight = 21834.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.060367 restraints weight = 20531.950| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10845 Z= 0.122 Angle : 0.590 8.848 14730 Z= 0.309 Chirality : 0.045 0.189 1650 Planarity : 0.004 0.036 1917 Dihedral : 4.344 36.315 1443 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -0.43 (0.22), residues: 1323 helix: 1.67 (0.25), residues: 408 sheet: -0.22 (0.32), residues: 246 loop : -1.62 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 124 TYR 0.007 0.001 TYR E 308 PHE 0.018 0.001 PHE D 63 TRP 0.021 0.001 TRP E 222 HIS 0.008 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10824) covalent geometry : angle 0.58840 / 0.31 (14685) SS BOND : bond 0.00574 / 0.34 ( 18) SS BOND : angle 1.06217 / 0.80 ( 36) hydrogen bonds : bond 0.03166 / 2.21 ( 483) hydrogen bonds : angle 4.29441 / 2.98 ( 1359) link_NAG-ASN : bond 0.00218 / 0.11 ( 3) link_NAG-ASN : angle 1.06639 / 0.51 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9289 (m-40) cc_final: 0.8471 (p0) REVERT: A 177 LEU cc_start: 0.8955 (mm) cc_final: 0.8561 (mm) REVERT: A 260 MET cc_start: 0.7164 (ppp) cc_final: 0.6734 (ptm) REVERT: A 280 GLU cc_start: 0.8858 (mp0) cc_final: 0.8415 (pm20) REVERT: A 288 ILE cc_start: 0.8975 (mt) cc_final: 0.8541 (mt) REVERT: B 63 PHE cc_start: 0.9126 (m-10) cc_final: 0.8706 (m-80) REVERT: B 64 HIS cc_start: 0.8694 (m170) cc_final: 0.8121 (m90) REVERT: B 66 ILE cc_start: 0.9660 (mt) cc_final: 0.9052 (mt) REVERT: B 68 LYS cc_start: 0.9397 (mmtm) cc_final: 0.9137 (mmtm) REVERT: B 69 GLU cc_start: 0.8869 (mp0) cc_final: 0.8653 (mp0) REVERT: B 70 PHE cc_start: 0.8583 (m-80) cc_final: 0.8068 (m-80) REVERT: B 86 ASP cc_start: 0.8488 (t0) cc_final: 0.7947 (t0) REVERT: B 90 ASP cc_start: 0.8959 (m-30) cc_final: 0.8704 (m-30) REVERT: B 133 MET cc_start: 0.7827 (ptt) cc_final: 0.7465 (ppp) REVERT: C 70 LEU cc_start: 0.7518 (tp) cc_final: 0.7189 (mt) REVERT: C 98 TYR cc_start: 0.8960 (t80) cc_final: 0.8437 (t80) REVERT: C 137 ASN cc_start: 0.9327 (m-40) cc_final: 0.8753 (p0) REVERT: C 231 SER cc_start: 0.8402 (m) cc_final: 0.7688 (m) REVERT: C 233 TYR cc_start: 0.8273 (m-80) cc_final: 0.7961 (m-80) REVERT: C 320 MET cc_start: 0.5697 (ptm) cc_final: 0.5491 (ptm) REVERT: E 50 LYS cc_start: 0.8740 (mttt) cc_final: 0.8101 (mmmt) REVERT: E 260 MET cc_start: 0.6869 (ptp) cc_final: 0.6657 (pmm) REVERT: D 39 LYS cc_start: 0.9718 (mmtm) cc_final: 0.9472 (mmmt) REVERT: D 42 GLN cc_start: 0.9455 (mt0) cc_final: 0.9007 (mt0) REVERT: D 54 ARG cc_start: 0.9143 (mtp85) cc_final: 0.8893 (mtp-110) REVERT: D 59 THR cc_start: 0.9341 (p) cc_final: 0.8879 (p) REVERT: D 62 LYS cc_start: 0.9201 (mptt) cc_final: 0.9000 (mmtt) REVERT: D 63 PHE cc_start: 0.9024 (m-10) cc_final: 0.8775 (m-80) REVERT: D 64 HIS cc_start: 0.8820 (m170) cc_final: 0.8366 (m90) REVERT: D 86 ASP cc_start: 0.8407 (t0) cc_final: 0.7898 (t0) REVERT: D 90 ASP cc_start: 0.8759 (m-30) cc_final: 0.8474 (m-30) REVERT: D 133 MET cc_start: 0.7987 (ptt) cc_final: 0.7642 (mpp) REVERT: F 39 LYS cc_start: 0.9698 (mmtm) cc_final: 0.9403 (mmmt) REVERT: F 42 GLN cc_start: 0.9408 (mt0) cc_final: 0.8919 (mt0) REVERT: F 59 THR cc_start: 0.9423 (p) cc_final: 0.8342 (p) REVERT: F 63 PHE cc_start: 0.9081 (m-10) cc_final: 0.8831 (m-80) REVERT: F 66 ILE cc_start: 0.9545 (mt) cc_final: 0.9191 (mt) REVERT: F 68 LYS cc_start: 0.9438 (ptmt) cc_final: 0.9015 (pttp) REVERT: F 70 PHE cc_start: 0.8547 (m-80) cc_final: 0.8150 (m-80) REVERT: F 86 ASP cc_start: 0.8391 (t0) cc_final: 0.7737 (t0) REVERT: F 90 ASP cc_start: 0.8976 (m-30) cc_final: 0.8624 (m-30) REVERT: F 133 MET cc_start: 0.7871 (ptt) cc_final: 0.7578 (mpp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1080 time to fit residues: 27.2766 Evaluate side-chains 154 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.4980 chunk 85 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 28 optimal weight: 0.0050 chunk 45 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 ASN B 104 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.088326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.061730 restraints weight = 51592.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.059497 restraints weight = 28201.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.060065 restraints weight = 27252.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.060304 restraints weight = 22058.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.060381 restraints weight = 21002.976| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10845 Z= 0.114 Angle : 0.575 9.048 14730 Z= 0.303 Chirality : 0.044 0.180 1650 Planarity : 0.004 0.036 1917 Dihedral : 4.235 34.259 1443 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -0.25 (0.22), residues: 1323 helix: 1.86 (0.25), residues: 405 sheet: -0.10 (0.33), residues: 246 loop : -1.54 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 127 TYR 0.007 0.001 TYR E 308 PHE 0.012 0.001 PHE E 147 TRP 0.022 0.001 TRP E 222 HIS 0.007 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10824) covalent geometry : angle 0.57309 / 0.30 (14685) SS BOND : bond 0.00524 / 0.32 ( 18) SS BOND : angle 1.00772 / 0.75 ( 36) hydrogen bonds : bond 0.03109 / 2.17 ( 483) hydrogen bonds : angle 4.24866 / 2.94 ( 1359) link_NAG-ASN : bond 0.00237 / 0.12 ( 3) link_NAG-ASN : angle 1.04378 / 0.51 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2160.33 seconds wall clock time: 38 minutes 4.69 seconds (2284.69 seconds total)