Starting phenix.real_space_refine on Wed Jun 3 14:50:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yyv_73657/06_2026/9yyv_73657.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yyv_73657/06_2026/9yyv_73657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yyv_73657/06_2026/9yyv_73657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yyv_73657/06_2026/9yyv_73657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yyv_73657/06_2026/9yyv_73657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yyv_73657/06_2026/9yyv_73657.map" } resolution = 3.3 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= -0.000 sd= 0.041 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 30 5.16 5 C 4116 2.51 5 N 1101 2.21 5 O 1179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6426 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2072 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Restraints were copied for chains: B, C Time building chain proxies: 1.65, per 1000 atoms: 0.26 Number of scatterers: 6426 At special positions: 0 Unit cell: (72.3684, 72.3684, 172.571, 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 30 16.00 O 1179 8.00 N 1101 7.00 C 4116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " 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 A1301 " - " ASN A1098 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 717 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A 709 " " NAG B1301 " - " ASN B1098 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 717 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B 709 " " NAG C1301 " - " ASN C1098 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 717 " " NAG C1304 " - " ASN C 801 " " NAG C1305 " - " ASN C 709 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 355.3 milliseconds 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1614 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 12 sheets defined 45.4% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.676A pdb=" N ALA A 706 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.574A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.864A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 1033 removed outlier: 3.736A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 708 removed outlier: 3.676A pdb=" N ALA B 706 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.574A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 769 removed outlier: 3.864A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 1033 removed outlier: 3.737A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 708 removed outlier: 3.676A pdb=" N ALA C 706 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.574A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 769 removed outlier: 3.865A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 1033 removed outlier: 3.736A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 713 through 718 removed outlier: 6.721A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 721 through 728 removed outlier: 3.500A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1087 through 1090 removed outlier: 3.501A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.663A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 713 through 718 removed outlier: 6.721A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 721 through 728 removed outlier: 3.500A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1087 through 1090 removed outlier: 3.502A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.664A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 713 through 718 removed outlier: 6.721A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.501A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1087 through 1090 removed outlier: 3.501A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.663A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1035 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: 0.92 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1718 1.33 - 1.45: 1164 1.45 - 1.57: 3616 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 6540 Sorted by residual: bond pdb=" CA CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sigma weight residual 1.524 1.537 -0.014 1.33e-02 5.65e+03 1.08e+00 bond pdb=" CA CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sigma weight residual 1.524 1.537 -0.014 1.33e-02 5.65e+03 1.07e+00 bond pdb=" CA CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.33e-02 5.65e+03 1.01e+00 bond pdb=" CG ASN A 709 " pdb=" ND2 ASN A 709 " ideal model delta sigma weight residual 1.328 1.345 -0.017 2.10e-02 2.27e+03 6.56e-01 bond pdb=" CG ASN B 709 " pdb=" ND2 ASN B 709 " ideal model delta sigma weight residual 1.328 1.345 -0.017 2.10e-02 2.27e+03 6.35e-01 ... (remaining 6535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 8688 1.29 - 2.58: 202 2.58 - 3.87: 29 3.87 - 5.16: 3 5.16 - 6.45: 6 Bond angle restraints: 8928 Sorted by residual: angle pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " pdb=" CG ASN A 709 " ideal model delta sigma weight residual 112.60 114.94 -2.34 1.00e+00 1.00e+00 5.48e+00 angle pdb=" CA ASN B 709 " pdb=" CB ASN B 709 " pdb=" CG ASN B 709 " ideal model delta sigma weight residual 112.60 114.90 -2.30 1.00e+00 1.00e+00 5.28e+00 angle pdb=" CA ASN C 709 " pdb=" CB ASN C 709 " pdb=" CG ASN C 709 " ideal model delta sigma weight residual 112.60 114.86 -2.26 1.00e+00 1.00e+00 5.09e+00 angle pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " pdb=" C5 NAG C1305 " ideal model delta sigma weight residual 113.21 106.76 6.45 3.00e+00 1.11e-01 4.63e+00 angle pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " pdb=" C5 NAG A1305 " ideal model delta sigma weight residual 113.21 106.77 6.44 3.00e+00 1.11e-01 4.61e+00 ... (remaining 8923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3666 17.97 - 35.94: 285 35.94 - 53.91: 96 53.91 - 71.87: 24 71.87 - 89.84: 6 Dihedral angle restraints: 4077 sinusoidal: 1596 harmonic: 2481 Sorted by residual: dihedral pdb=" CA ASN C 709 " pdb=" C ASN C 709 " pdb=" N ASN C 710 " pdb=" CA ASN C 710 " ideal model delta harmonic sigma weight residual -180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ASN B 709 " pdb=" C ASN B 709 " pdb=" N ASN B 710 " pdb=" CA ASN B 710 " ideal model delta harmonic sigma weight residual 180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ASN A 709 " pdb=" C ASN A 709 " pdb=" N ASN A 710 " pdb=" CA ASN A 710 " ideal model delta harmonic sigma weight residual -180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 4074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1110 0.116 - 0.232: 9 0.232 - 0.348: 3 0.348 - 0.465: 0 0.465 - 0.581: 3 Chirality restraints: 1125 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.36e+00 ... (remaining 1122 not shown) Planarity restraints: 1149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " 0.031 2.00e-02 2.50e+03 3.03e-02 1.15e+01 pdb=" CG ASN C 709 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " -0.028 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.031 2.00e-02 2.50e+03 3.00e-02 1.13e+01 pdb=" CG ASN B 709 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " 0.031 2.00e-02 2.50e+03 2.99e-02 1.12e+01 pdb=" CG ASN A 709 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " -0.028 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.028 2.00e-02 2.50e+03 ... (remaining 1146 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2421 2.89 - 3.40: 5909 3.40 - 3.90: 10406 3.90 - 4.40: 10949 4.40 - 4.90: 19383 Nonbonded interactions: 49068 Sorted by model distance: nonbonded pdb=" O4 NAG C1305 " pdb=" O6 NAG C1305 " model vdw 2.393 3.040 nonbonded pdb=" O4 NAG A1305 " pdb=" O6 NAG A1305 " model vdw 2.393 3.040 nonbonded pdb=" O4 NAG B1305 " pdb=" O6 NAG B1305 " model vdw 2.394 3.040 nonbonded pdb=" NE ARG A 995 " pdb=" OD2 ASP C 994 " model vdw 2.485 3.120 nonbonded pdb=" OD2 ASP A 994 " pdb=" NE ARG B 995 " model vdw 2.485 3.120 ... (remaining 49063 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.720 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.002 0.020 6564 Z= 0.100 Angle : 0.559 10.545 8991 Z= 0.270 Chirality : 0.052 0.581 1125 Planarity : 0.002 0.020 1134 Dihedral : 15.692 89.843 2436 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 17.53 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.29), residues: 834 helix: 4.03 (0.25), residues: 336 sheet: 1.79 (0.55), residues: 90 loop : -0.21 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1000 TYR 0.030 0.002 TYR C1110 PHE 0.005 0.001 PHE A 800 TRP 0.001 0.000 TRP A1102 HIS 0.001 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.10 ( 6540) covalent geometry : angle 0.47874 / 0.25 ( 8928) SS BOND : bond 0.00067 / 0.04 ( 9) SS BOND : angle 0.39809 / 0.26 ( 18) hydrogen bonds : bond 0.14081 / 9.50 ( 363) hydrogen bonds : angle 6.12205 / 4.50 ( 1035) link_NAG-ASN : bond 0.01109 / 0.75 ( 15) link_NAG-ASN : angle 4.10911 / 2.75 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.234 Fit side-chains REVERT: A 1047 TYR cc_start: 0.8849 (m-80) cc_final: 0.8627 (m-80) REVERT: B 720 ILE cc_start: 0.7898 (mm) cc_final: 0.7560 (tp) REVERT: B 1014 ARG cc_start: 0.8217 (ttt90) cc_final: 0.7934 (tpt-90) REVERT: B 1038 LYS cc_start: 0.8733 (mmtm) cc_final: 0.8380 (mmtm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1126 time to fit residues: 10.0967 Evaluate side-chains 66 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0030 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 GLN B 774 GLN B1054 GLN B1058 HIS C1054 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120927 restraints weight = 8301.562| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.12 r_work: 0.3253 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6564 Z= 0.178 Angle : 0.533 5.411 8991 Z= 0.268 Chirality : 0.043 0.233 1125 Planarity : 0.003 0.031 1134 Dihedral : 4.001 17.565 1209 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.55 % Allowed : 14.95 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.29), residues: 834 helix: 4.01 (0.25), residues: 339 sheet: 1.00 (0.45), residues: 120 loop : -0.55 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1014 TYR 0.025 0.002 TYR A1110 PHE 0.017 0.002 PHE C 800 TRP 0.005 0.001 TRP B1102 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 6540) covalent geometry : angle 0.50423 / 0.26 ( 8928) SS BOND : bond 0.00086 / 0.06 ( 9) SS BOND : angle 1.11542 / 0.74 ( 18) hydrogen bonds : bond 0.05837 / 4.12 ( 363) hydrogen bonds : angle 4.36538 / 3.22 ( 1035) link_NAG-ASN : bond 0.00418 / 0.29 ( 15) link_NAG-ASN : angle 2.40514 / 1.59 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.240 Fit side-chains REVERT: A 1113 GLN cc_start: 0.7551 (mt0) cc_final: 0.7340 (mt0) REVERT: B 720 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8254 (tp) REVERT: B 1038 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8647 (mmtm) REVERT: B 1073 LYS cc_start: 0.7104 (ptmm) cc_final: 0.6809 (ttpt) outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.1265 time to fit residues: 11.1414 Evaluate side-chains 67 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN B1058 HIS C 774 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116808 restraints weight = 8437.739| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.10 r_work: 0.3210 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6564 Z= 0.172 Angle : 0.510 5.222 8991 Z= 0.256 Chirality : 0.041 0.165 1125 Planarity : 0.003 0.020 1134 Dihedral : 4.113 20.374 1209 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.55 % Allowed : 16.15 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.29), residues: 834 helix: 3.88 (0.25), residues: 339 sheet: 0.82 (0.44), residues: 120 loop : -0.57 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1000 TYR 0.013 0.002 TYR B1047 PHE 0.014 0.002 PHE C 800 TRP 0.003 0.001 TRP B1102 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 6540) covalent geometry : angle 0.48825 / 0.25 ( 8928) SS BOND : bond 0.00138 / 0.09 ( 9) SS BOND : angle 1.11139 / 0.72 ( 18) hydrogen bonds : bond 0.05623 / 3.97 ( 363) hydrogen bonds : angle 4.25167 / 3.13 ( 1035) link_NAG-ASN : bond 0.00328 / 0.23 ( 15) link_NAG-ASN : angle 2.06321 / 1.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.188 Fit side-chains REVERT: A 1113 GLN cc_start: 0.7707 (mt0) cc_final: 0.7446 (mt0) REVERT: B 1038 LYS cc_start: 0.8979 (mmtm) cc_final: 0.8615 (mmtt) REVERT: B 1073 LYS cc_start: 0.7423 (ptmm) cc_final: 0.7075 (ttpt) REVERT: C 727 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8949 (mt) REVERT: C 1073 LYS cc_start: 0.7535 (pttt) cc_final: 0.7218 (ptmm) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 0.1338 time to fit residues: 12.1052 Evaluate side-chains 71 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 727 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 0.0970 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS A1088 HIS B1058 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119689 restraints weight = 8516.354| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.10 r_work: 0.3050 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6564 Z= 0.124 Angle : 0.450 4.951 8991 Z= 0.226 Chirality : 0.040 0.140 1125 Planarity : 0.003 0.020 1134 Dihedral : 3.814 19.672 1209 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.72 % Allowed : 17.70 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.29), residues: 834 helix: 4.16 (0.24), residues: 339 sheet: 0.88 (0.44), residues: 120 loop : -0.53 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1000 TYR 0.013 0.002 TYR C1067 PHE 0.010 0.001 PHE C 800 TRP 0.001 0.000 TRP A1102 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6540) covalent geometry : angle 0.42711 / 0.22 ( 8928) SS BOND : bond 0.00113 / 0.08 ( 9) SS BOND : angle 0.86217 / 0.57 ( 18) hydrogen bonds : bond 0.05164 / 3.64 ( 363) hydrogen bonds : angle 3.93751 / 2.89 ( 1035) link_NAG-ASN : bond 0.00283 / 0.19 ( 15) link_NAG-ASN : angle 2.00988 / 1.33 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.227 Fit side-chains REVERT: A 1113 GLN cc_start: 0.7640 (mt0) cc_final: 0.7379 (mt0) REVERT: B 1038 LYS cc_start: 0.8944 (mmtm) cc_final: 0.8695 (mmtm) REVERT: B 1073 LYS cc_start: 0.7361 (ptmm) cc_final: 0.6989 (ttpt) REVERT: B 1113 GLN cc_start: 0.8014 (mp10) cc_final: 0.7543 (mp10) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.1310 time to fit residues: 12.1124 Evaluate side-chains 71 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS B1058 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117901 restraints weight = 8466.566| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.09 r_work: 0.3029 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6564 Z= 0.136 Angle : 0.459 5.284 8991 Z= 0.230 Chirality : 0.040 0.134 1125 Planarity : 0.003 0.040 1134 Dihedral : 3.821 20.120 1209 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.41 % Allowed : 17.35 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.28), residues: 834 helix: 4.16 (0.24), residues: 339 sheet: 1.63 (0.53), residues: 90 loop : -0.32 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 995 TYR 0.013 0.002 TYR C1067 PHE 0.011 0.001 PHE C 800 TRP 0.001 0.000 TRP A1102 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 6540) covalent geometry : angle 0.43499 / 0.22 ( 8928) SS BOND : bond 0.00108 / 0.07 ( 9) SS BOND : angle 0.84412 / 0.56 ( 18) hydrogen bonds : bond 0.05207 / 3.67 ( 363) hydrogen bonds : angle 3.95332 / 2.90 ( 1035) link_NAG-ASN : bond 0.00301 / 0.21 ( 15) link_NAG-ASN : angle 2.08732 / 1.38 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.294 Fit side-chains REVERT: B 1038 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8703 (mmtm) REVERT: B 1073 LYS cc_start: 0.7373 (ptmm) cc_final: 0.7022 (ttpt) REVERT: C 986 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7947 (ttpt) REVERT: C 1073 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7058 (ttpt) outliers start: 14 outliers final: 10 residues processed: 78 average time/residue: 0.1396 time to fit residues: 12.9901 Evaluate side-chains 77 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS B1058 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115553 restraints weight = 8528.531| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.09 r_work: 0.3197 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6564 Z= 0.170 Angle : 0.493 5.734 8991 Z= 0.247 Chirality : 0.040 0.131 1125 Planarity : 0.003 0.022 1134 Dihedral : 4.086 21.729 1209 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.06 % Allowed : 18.38 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.28), residues: 834 helix: 4.02 (0.25), residues: 339 sheet: 1.43 (0.52), residues: 90 loop : -0.35 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1107 TYR 0.013 0.002 TYR B1047 PHE 0.012 0.001 PHE C 800 TRP 0.001 0.001 TRP B1102 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 6540) covalent geometry : angle 0.46614 / 0.24 ( 8928) SS BOND : bond 0.00118 / 0.08 ( 9) SS BOND : angle 0.87103 / 0.58 ( 18) hydrogen bonds : bond 0.05413 / 3.83 ( 363) hydrogen bonds : angle 4.05512 / 2.98 ( 1035) link_NAG-ASN : bond 0.00298 / 0.21 ( 15) link_NAG-ASN : angle 2.26009 / 1.50 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.205 Fit side-chains REVERT: B 1038 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8712 (mmtm) REVERT: B 1073 LYS cc_start: 0.7101 (ptmm) cc_final: 0.6844 (ttpt) REVERT: B 1113 GLN cc_start: 0.8148 (mp10) cc_final: 0.7187 (mp10) REVERT: C 986 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8142 (ttpt) REVERT: C 1073 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7286 (ttpt) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.1388 time to fit residues: 12.5221 Evaluate side-chains 75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS B1058 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115171 restraints weight = 8512.746| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.06 r_work: 0.3190 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6564 Z= 0.175 Angle : 0.496 6.019 8991 Z= 0.248 Chirality : 0.040 0.135 1125 Planarity : 0.003 0.021 1134 Dihedral : 4.259 23.324 1209 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.06 % Allowed : 18.56 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.46 (0.29), residues: 834 helix: 3.95 (0.25), residues: 339 sheet: 1.29 (0.52), residues: 90 loop : -0.39 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.015 0.002 TYR A1110 PHE 0.013 0.001 PHE C 800 TRP 0.002 0.001 TRP A1102 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 6540) covalent geometry : angle 0.46747 / 0.24 ( 8928) SS BOND : bond 0.00119 / 0.08 ( 9) SS BOND : angle 0.85614 / 0.57 ( 18) hydrogen bonds : bond 0.05443 / 3.85 ( 363) hydrogen bonds : angle 4.06200 / 2.98 ( 1035) link_NAG-ASN : bond 0.00309 / 0.21 ( 15) link_NAG-ASN : angle 2.34283 / 1.55 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.150 Fit side-chains REVERT: A 1107 ARG cc_start: 0.8303 (ttt-90) cc_final: 0.7932 (tpt90) REVERT: B 1073 LYS cc_start: 0.7167 (ptmm) cc_final: 0.6947 (ttpt) REVERT: B 1113 GLN cc_start: 0.8116 (mp10) cc_final: 0.7179 (mp10) REVERT: C 986 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8101 (ttpt) REVERT: C 1073 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7241 (ttpt) outliers start: 12 outliers final: 11 residues processed: 74 average time/residue: 0.1304 time to fit residues: 11.5644 Evaluate side-chains 75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 68 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS B1058 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117408 restraints weight = 8506.667| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.06 r_work: 0.3211 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6564 Z= 0.124 Angle : 0.449 6.054 8991 Z= 0.226 Chirality : 0.040 0.153 1125 Planarity : 0.003 0.024 1134 Dihedral : 4.031 20.823 1209 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.89 % Allowed : 19.42 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.29), residues: 834 helix: 4.19 (0.24), residues: 339 sheet: 1.38 (0.53), residues: 90 loop : -0.35 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1107 TYR 0.015 0.002 TYR C1067 PHE 0.010 0.001 PHE C 800 TRP 0.003 0.001 TRP A1102 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6540) covalent geometry : angle 0.42066 / 0.22 ( 8928) SS BOND : bond 0.00103 / 0.07 ( 9) SS BOND : angle 0.75384 / 0.50 ( 18) hydrogen bonds : bond 0.05140 / 3.63 ( 363) hydrogen bonds : angle 3.89327 / 2.86 ( 1035) link_NAG-ASN : bond 0.00315 / 0.22 ( 15) link_NAG-ASN : angle 2.23455 / 1.49 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.229 Fit side-chains REVERT: A 1107 ARG cc_start: 0.8323 (ttt-90) cc_final: 0.7783 (tpt90) REVERT: B 1073 LYS cc_start: 0.7075 (ptmm) cc_final: 0.6852 (ttpt) REVERT: B 1113 GLN cc_start: 0.8133 (mp10) cc_final: 0.7150 (mp10) REVERT: C 986 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8088 (ttpt) REVERT: C 1073 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7124 (ttpt) outliers start: 11 outliers final: 10 residues processed: 74 average time/residue: 0.1354 time to fit residues: 12.0667 Evaluate side-chains 76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.0060 chunk 76 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 37 optimal weight: 0.0060 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 overall best weight: 0.2612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1058 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120178 restraints weight = 8606.150| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.11 r_work: 0.3240 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 6564 Z= 0.106 Angle : 0.427 5.996 8991 Z= 0.215 Chirality : 0.039 0.164 1125 Planarity : 0.003 0.027 1134 Dihedral : 3.704 19.706 1209 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.06 % Allowed : 19.93 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.29), residues: 834 helix: 4.32 (0.24), residues: 339 sheet: 1.48 (0.52), residues: 90 loop : -0.31 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1000 TYR 0.015 0.002 TYR C1067 PHE 0.008 0.001 PHE C 800 TRP 0.003 0.001 TRP A1102 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 6540) covalent geometry : angle 0.39880 / 0.21 ( 8928) SS BOND : bond 0.00090 / 0.06 ( 9) SS BOND : angle 0.68936 / 0.46 ( 18) hydrogen bonds : bond 0.04886 / 3.44 ( 363) hydrogen bonds : angle 3.73325 / 2.73 ( 1035) link_NAG-ASN : bond 0.00327 / 0.22 ( 15) link_NAG-ASN : angle 2.16192 / 1.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.246 Fit side-chains REVERT: A 1014 ARG cc_start: 0.8195 (ttt90) cc_final: 0.7763 (tpt170) REVERT: A 1107 ARG cc_start: 0.8215 (ttt-90) cc_final: 0.7724 (tpt90) REVERT: B 974 SER cc_start: 0.8408 (t) cc_final: 0.8161 (p) REVERT: B 1038 LYS cc_start: 0.8911 (mmtm) cc_final: 0.8589 (mmtt) REVERT: B 1073 LYS cc_start: 0.7018 (ptmm) cc_final: 0.6779 (ttpt) REVERT: B 1113 GLN cc_start: 0.8112 (mp10) cc_final: 0.7119 (mp10) REVERT: C 986 LYS cc_start: 0.8317 (ttpt) cc_final: 0.8060 (ttpt) REVERT: C 1073 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7057 (ptmm) outliers start: 12 outliers final: 8 residues processed: 79 average time/residue: 0.1207 time to fit residues: 11.5124 Evaluate side-chains 75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.5980 chunk 37 optimal weight: 0.0010 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS B1058 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117373 restraints weight = 8403.280| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.04 r_work: 0.3227 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6564 Z= 0.137 Angle : 0.455 5.955 8991 Z= 0.229 Chirality : 0.040 0.151 1125 Planarity : 0.003 0.048 1134 Dihedral : 3.837 20.498 1209 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.55 % Allowed : 20.10 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.29), residues: 834 helix: 4.20 (0.24), residues: 339 sheet: 1.43 (0.52), residues: 90 loop : -0.35 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 995 TYR 0.014 0.002 TYR C1067 PHE 0.010 0.001 PHE C 800 TRP 0.002 0.001 TRP A1102 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6540) covalent geometry : angle 0.42631 / 0.22 ( 8928) SS BOND : bond 0.00095 / 0.06 ( 9) SS BOND : angle 0.78373 / 0.52 ( 18) hydrogen bonds : bond 0.05114 / 3.62 ( 363) hydrogen bonds : angle 3.84674 / 2.82 ( 1035) link_NAG-ASN : bond 0.00299 / 0.20 ( 15) link_NAG-ASN : angle 2.23854 / 1.49 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.232 Fit side-chains REVERT: A 1107 ARG cc_start: 0.8343 (ttt-90) cc_final: 0.7818 (tpt90) REVERT: B 1073 LYS cc_start: 0.7090 (ptmm) cc_final: 0.6867 (ttpt) REVERT: B 1113 GLN cc_start: 0.8115 (mp10) cc_final: 0.7133 (mp10) REVERT: C 986 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8093 (ttpt) REVERT: C 1073 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7142 (ptmm) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.1354 time to fit residues: 11.7557 Evaluate side-chains 74 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.0060 chunk 17 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1058 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.117871 restraints weight = 8551.920| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.07 r_work: 0.3237 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 6564 Z= 0.119 Angle : 0.437 6.004 8991 Z= 0.220 Chirality : 0.039 0.157 1125 Planarity : 0.003 0.024 1134 Dihedral : 3.794 19.949 1209 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.55 % Allowed : 20.10 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.29), residues: 834 helix: 4.27 (0.24), residues: 339 sheet: 1.47 (0.52), residues: 90 loop : -0.34 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1107 TYR 0.015 0.002 TYR C1067 PHE 0.009 0.001 PHE C 800 TRP 0.003 0.001 TRP A1102 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6540) covalent geometry : angle 0.40829 / 0.21 ( 8928) SS BOND : bond 0.00096 / 0.07 ( 9) SS BOND : angle 0.72677 / 0.48 ( 18) hydrogen bonds : bond 0.04999 / 3.53 ( 363) hydrogen bonds : angle 3.77678 / 2.77 ( 1035) link_NAG-ASN : bond 0.00311 / 0.21 ( 15) link_NAG-ASN : angle 2.19525 / 1.47 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1661.15 seconds wall clock time: 29 minutes 16.99 seconds (1756.99 seconds total)