Starting phenix.real_space_refine on Fri Oct 23 04:28:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k48_22661/10_2026/7k48_22661.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k48_22661/10_2026/7k48_22661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k48_22661/10_2026/7k48_22661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k48_22661/10_2026/7k48_22661.map" model { file = "/net/cci-nas-00/data/ceres_data/7k48_22661/10_2026/7k48_22661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k48_22661/10_2026/7k48_22661.cif" } resolution = 3.6 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= 0.069 sd= 0.926 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 80 5.16 5 C 5696 2.51 5 N 1316 2.21 5 O 1388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8480 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1858 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "E" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 262 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 1.53, per 1000 atoms: 0.18 Number of scatterers: 8480 At special positions: 0 Unit cell: (123.552, 123.552, 72.864, 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 80 16.00 O 1388 8.00 N 1316 7.00 C 5696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 17 " distance=2.02 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 24 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 31 " distance=2.02 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 17 " distance=2.02 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 24 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 31 " distance=2.02 Simple disulfide: pdb=" SG CYS G 2 " - pdb=" SG CYS G 17 " distance=2.02 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 24 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 31 " distance=2.02 Simple disulfide: pdb=" SG CYS H 2 " - pdb=" SG CYS H 17 " distance=2.02 Simple disulfide: pdb=" SG CYS H 9 " - pdb=" SG CYS H 24 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 31 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 326.7 milliseconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 79.1% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 720 through 732 Processing helix chain 'A' and resid 732 through 751 Processing helix chain 'A' and resid 758 through 787 removed outlier: 3.625A pdb=" N ASN A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.901A pdb=" N ASP A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 811 Processing helix chain 'A' and resid 818 through 829 Processing helix chain 'A' and resid 830 through 835 Processing helix chain 'A' and resid 837 through 876 removed outlier: 4.125A pdb=" N LYS A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) Proline residue: A 852 - end of helix Processing helix chain 'A' and resid 880 through 885 removed outlier: 3.929A pdb=" N PHE A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.599A pdb=" N VAL A 914 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 948 Proline residue: A 924 - end of helix removed outlier: 4.877A pdb=" N ASP A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ALA A 944 " --> pdb=" O ILE A 940 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 732 Processing helix chain 'B' and resid 732 through 751 Processing helix chain 'B' and resid 758 through 787 removed outlier: 3.624A pdb=" N ASN B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 removed outlier: 3.901A pdb=" N ASP B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 811 Processing helix chain 'B' and resid 818 through 829 Processing helix chain 'B' and resid 830 through 835 Processing helix chain 'B' and resid 837 through 876 removed outlier: 4.126A pdb=" N LYS B 842 " --> pdb=" O PRO B 838 " (cutoff:3.500A) Proline residue: B 852 - end of helix Processing helix chain 'B' and resid 880 through 885 removed outlier: 3.928A pdb=" N PHE B 884 " --> pdb=" O PHE B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 899 Processing helix chain 'B' and resid 907 through 915 removed outlier: 3.599A pdb=" N VAL B 914 " --> pdb=" O PRO B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 948 Proline residue: B 924 - end of helix removed outlier: 4.877A pdb=" N ASP B 943 " --> pdb=" O ALA B 939 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA B 944 " --> pdb=" O ILE B 940 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET B 945 " --> pdb=" O ILE B 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 732 Processing helix chain 'C' and resid 732 through 751 Processing helix chain 'C' and resid 758 through 787 removed outlier: 3.624A pdb=" N ASN C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 removed outlier: 3.901A pdb=" N ASP C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 811 Processing helix chain 'C' and resid 818 through 829 Processing helix chain 'C' and resid 830 through 835 Processing helix chain 'C' and resid 837 through 876 removed outlier: 4.125A pdb=" N LYS C 842 " --> pdb=" O PRO C 838 " (cutoff:3.500A) Proline residue: C 852 - end of helix Processing helix chain 'C' and resid 880 through 885 removed outlier: 3.928A pdb=" N PHE C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 899 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.599A pdb=" N VAL C 914 " --> pdb=" O PRO C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 948 Proline residue: C 924 - end of helix removed outlier: 4.877A pdb=" N ASP C 943 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA C 944 " --> pdb=" O ILE C 940 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET C 945 " --> pdb=" O ILE C 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 732 Processing helix chain 'D' and resid 732 through 751 Processing helix chain 'D' and resid 758 through 787 removed outlier: 3.624A pdb=" N ASN D 763 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL D 764 " --> pdb=" O GLU D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 removed outlier: 3.902A pdb=" N ASP D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 811 Processing helix chain 'D' and resid 818 through 829 Processing helix chain 'D' and resid 830 through 835 Processing helix chain 'D' and resid 837 through 876 removed outlier: 4.125A pdb=" N LYS D 842 " --> pdb=" O PRO D 838 " (cutoff:3.500A) Proline residue: D 852 - end of helix Processing helix chain 'D' and resid 880 through 885 removed outlier: 3.929A pdb=" N PHE D 884 " --> pdb=" O PHE D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 899 Processing helix chain 'D' and resid 907 through 915 removed outlier: 3.598A pdb=" N VAL D 914 " --> pdb=" O PRO D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 948 Proline residue: D 924 - end of helix removed outlier: 4.877A pdb=" N ASP D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA D 944 " --> pdb=" O ILE D 940 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET D 945 " --> pdb=" O ILE D 941 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 20 Processing helix chain 'F' and resid 17 through 20 Processing helix chain 'G' and resid 17 through 20 Processing helix chain 'H' and resid 17 through 20 Processing sheet with id=AA1, first strand: chain 'E' and resid 22 through 24 removed outlier: 3.612A pdb=" N VAL E 23 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 22 through 24 removed outlier: 3.612A pdb=" N VAL F 23 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 22 through 24 removed outlier: 3.612A pdb=" N VAL G 23 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 24 removed outlier: 3.613A pdb=" N VAL H 23 " --> pdb=" O LYS H 32 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1599 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: 1.18 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2475 1.35 - 1.47: 2411 1.47 - 1.60: 3690 1.60 - 1.72: 0 1.72 - 1.85: 132 Bond restraints: 8708 Sorted by residual: bond pdb=" C ILE D 851 " pdb=" N PRO D 852 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.20e-02 6.94e+03 2.11e+01 bond pdb=" C ILE A 851 " pdb=" N PRO A 852 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.20e-02 6.94e+03 2.08e+01 bond pdb=" C ILE C 851 " pdb=" N PRO C 852 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.05e+01 bond pdb=" C ILE B 851 " pdb=" N PRO B 852 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.04e+01 bond pdb=" C HIS D 755 " pdb=" N PRO D 756 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.68e+00 ... (remaining 8703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10959 2.10 - 4.20: 717 4.20 - 6.29: 96 6.29 - 8.39: 24 8.39 - 10.49: 20 Bond angle restraints: 11816 Sorted by residual: angle pdb=" CA ARG H 29 " pdb=" CB ARG H 29 " pdb=" CG ARG H 29 " ideal model delta sigma weight residual 114.10 124.34 -10.24 2.00e+00 2.50e-01 2.62e+01 angle pdb=" CA ARG F 29 " pdb=" CB ARG F 29 " pdb=" CG ARG F 29 " ideal model delta sigma weight residual 114.10 124.34 -10.24 2.00e+00 2.50e-01 2.62e+01 angle pdb=" CA ARG E 29 " pdb=" CB ARG E 29 " pdb=" CG ARG E 29 " ideal model delta sigma weight residual 114.10 124.30 -10.20 2.00e+00 2.50e-01 2.60e+01 angle pdb=" CA ARG G 29 " pdb=" CB ARG G 29 " pdb=" CG ARG G 29 " ideal model delta sigma weight residual 114.10 124.26 -10.16 2.00e+00 2.50e-01 2.58e+01 angle pdb=" C VAL A 928 " pdb=" N VAL A 929 " pdb=" CA VAL A 929 " ideal model delta sigma weight residual 121.02 115.09 5.93 1.51e+00 4.39e-01 1.54e+01 ... (remaining 11811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4372 17.90 - 35.81: 552 35.81 - 53.71: 125 53.71 - 71.62: 35 71.62 - 89.52: 20 Dihedral angle restraints: 5104 sinusoidal: 2016 harmonic: 3088 Sorted by residual: dihedral pdb=" CA VAL B 821 " pdb=" C VAL B 821 " pdb=" N LEU B 822 " pdb=" CA LEU B 822 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA VAL D 821 " pdb=" C VAL D 821 " pdb=" N LEU D 822 " pdb=" CA LEU D 822 " ideal model delta harmonic sigma weight residual 180.00 152.12 27.88 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA VAL A 821 " pdb=" C VAL A 821 " pdb=" N LEU A 822 " pdb=" CA LEU A 822 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 5101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 857 0.051 - 0.101: 376 0.101 - 0.152: 131 0.152 - 0.203: 18 0.203 - 0.253: 10 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CG LEU B 819 " pdb=" CB LEU B 819 " pdb=" CD1 LEU B 819 " pdb=" CD2 LEU B 819 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CG LEU A 819 " pdb=" CB LEU A 819 " pdb=" CD1 LEU A 819 " pdb=" CD2 LEU A 819 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CG LEU C 819 " pdb=" CB LEU C 819 " pdb=" CD1 LEU C 819 " pdb=" CD2 LEU C 819 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1389 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 901 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CD GLU B 901 " -0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU B 901 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU B 901 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 901 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CD GLU D 901 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU D 901 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU D 901 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 901 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CD GLU A 901 " -0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU A 901 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU A 901 " 0.020 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1792 2.77 - 3.30: 8773 3.30 - 3.83: 14308 3.83 - 4.37: 16301 4.37 - 4.90: 26092 Nonbonded interactions: 67266 Sorted by model distance: nonbonded pdb=" O TYR B 723 " pdb=" OG1 THR B 727 " model vdw 2.233 3.040 nonbonded pdb=" O TYR C 723 " pdb=" OG1 THR C 727 " model vdw 2.234 3.040 nonbonded pdb=" O TYR A 723 " pdb=" OG1 THR A 727 " model vdw 2.234 3.040 nonbonded pdb=" O TYR D 723 " pdb=" OG1 THR D 727 " model vdw 2.234 3.040 nonbonded pdb=" O ILE C 729 " pdb=" OG SER C 732 " model vdw 2.251 3.040 ... (remaining 67261 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 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 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: 1.780 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.080 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 : 0.010 0.063 8720 Z= 0.437 Angle : 1.231 10.492 11840 Z= 0.675 Chirality : 0.064 0.253 1392 Planarity : 0.009 0.079 1416 Dihedral : 17.881 89.520 3044 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.40 % Allowed : 14.47 % Favored : 82.13 % 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: -3.52 (0.21), residues: 1032 helix: -2.11 (0.15), residues: 712 sheet: None (None), residues: 0 loop : -2.43 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 26 TYR 0.022 0.004 TYR B 915 PHE 0.026 0.003 PHE C 772 TRP 0.028 0.004 TRP G 30 HIS 0.002 0.001 HIS A 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00953 / 0.44 ( 8708) covalent geometry : angle 1.22709 / 0.67 (11816) SS BOND : bond 0.00629 / 0.38 ( 12) SS BOND : angle 2.56818 / 1.34 ( 24) hydrogen bonds : bond 0.12817 / 8.52 ( 573) hydrogen bonds : angle 7.15893 / 5.14 ( 1599) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 325 time to evaluate : 0.233 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: A 866 TYR cc_start: 0.9143 (t80) cc_final: 0.8889 (t80) REVERT: A 867 ILE cc_start: 0.9186 (pt) cc_final: 0.8892 (mp) REVERT: A 874 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 898 MET cc_start: 0.8570 (tmm) cc_final: 0.7941 (tmm) REVERT: B 866 TYR cc_start: 0.8958 (t80) cc_final: 0.8671 (t80) REVERT: B 874 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8536 (tm-30) REVERT: B 898 MET cc_start: 0.8657 (tmm) cc_final: 0.8040 (tmm) REVERT: C 829 ARG cc_start: 0.8777 (mtp180) cc_final: 0.8446 (mtp180) REVERT: C 898 MET cc_start: 0.8662 (tmm) cc_final: 0.7998 (tmm) REVERT: D 748 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8908 (mm) REVERT: D 759 GLU cc_start: 0.8308 (tp30) cc_final: 0.7604 (pm20) REVERT: D 829 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8426 (mtp180) REVERT: D 898 MET cc_start: 0.8679 (tmm) cc_final: 0.8066 (tmm) outliers start: 32 outliers final: 11 residues processed: 337 average time/residue: 0.0908 time to fit residues: 41.3618 Evaluate side-chains 275 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 263 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 936 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45] chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN B 720 ASN C 720 ASN C 746 ASN D 720 ASN D 746 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.147505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.113941 restraints weight = 20190.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.117574 restraints weight = 8961.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.119767 restraints weight = 5432.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.120999 restraints weight = 4080.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.121506 restraints weight = 3511.107| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8720 Z= 0.157 Angle : 0.688 10.558 11840 Z= 0.353 Chirality : 0.040 0.126 1392 Planarity : 0.006 0.062 1416 Dihedral : 7.990 55.483 1130 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.00 % Allowed : 19.57 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.67 (0.25), residues: 1032 helix: -0.75 (0.18), residues: 712 sheet: -2.33 (0.71), residues: 36 loop : -1.45 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 783 TYR 0.018 0.002 TYR C 866 PHE 0.027 0.002 PHE B 831 TRP 0.015 0.001 TRP B 903 HIS 0.001 0.000 HIS B 754 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 ( 8708) covalent geometry : angle 0.68794 / 0.35 (11816) SS BOND : bond 0.00135 / 0.09 ( 12) SS BOND : angle 0.50686 / 0.32 ( 24) hydrogen bonds : bond 0.05237 / 3.58 ( 573) hydrogen bonds : angle 5.60926 / 4.04 ( 1599) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 0.328 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: A 748 LEU cc_start: 0.8994 (mm) cc_final: 0.8730 (mm) REVERT: A 752 MET cc_start: 0.8522 (mtt) cc_final: 0.7216 (mmt) REVERT: A 829 ARG cc_start: 0.8716 (mtp180) cc_final: 0.8315 (mtp85) REVERT: A 840 MET cc_start: 0.6908 (mmm) cc_final: 0.6478 (mmp) REVERT: A 866 TYR cc_start: 0.9062 (t80) cc_final: 0.8805 (t80) REVERT: A 871 MET cc_start: 0.9115 (mtp) cc_final: 0.8829 (mtp) REVERT: A 880 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8294 (p90) REVERT: A 898 MET cc_start: 0.8726 (tmm) cc_final: 0.8176 (tmm) REVERT: B 748 LEU cc_start: 0.9011 (mm) cc_final: 0.8655 (mm) REVERT: B 752 MET cc_start: 0.8693 (mtt) cc_final: 0.7359 (mmt) REVERT: B 829 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8227 (mmm-85) REVERT: B 866 TYR cc_start: 0.8899 (t80) cc_final: 0.8639 (t80) REVERT: B 867 ILE cc_start: 0.9061 (pt) cc_final: 0.8859 (mp) REVERT: B 874 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8413 (tm-30) REVERT: B 880 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8202 (p90) REVERT: B 898 MET cc_start: 0.8672 (tmm) cc_final: 0.8058 (tmm) REVERT: C 748 LEU cc_start: 0.9169 (mm) cc_final: 0.8908 (mm) REVERT: C 750 MET cc_start: 0.8590 (tpt) cc_final: 0.8308 (tpt) REVERT: C 779 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.9084 (pt0) REVERT: C 829 ARG cc_start: 0.8759 (mtp180) cc_final: 0.8470 (mtp180) REVERT: C 880 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7591 (p90) REVERT: C 898 MET cc_start: 0.8667 (tmm) cc_final: 0.8100 (tmm) REVERT: D 745 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9283 (mm) REVERT: D 748 LEU cc_start: 0.9166 (mm) cc_final: 0.8960 (mm) REVERT: D 750 MET cc_start: 0.8737 (tpt) cc_final: 0.8384 (tpt) REVERT: D 829 ARG cc_start: 0.8713 (mtp180) cc_final: 0.8155 (mmm-85) REVERT: D 866 TYR cc_start: 0.8881 (t80) cc_final: 0.8678 (t80) REVERT: D 880 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8166 (p90) REVERT: D 898 MET cc_start: 0.8697 (tmm) cc_final: 0.8147 (tmm) outliers start: 47 outliers final: 22 residues processed: 307 average time/residue: 0.0787 time to fit residues: 34.0543 Evaluate side-chains 298 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 880 PHE Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 935 ASN Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 880 PHE Chi-restraints excluded: chain D residue 929 VAL Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain H residue 2 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [29, 67, 16, 61, 39, 74, 5, 56, 91, 69, 18] chunk 29 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 746 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.145841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.111939 restraints weight = 20218.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.115514 restraints weight = 8945.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.117655 restraints weight = 5461.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.118573 restraints weight = 4142.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.119356 restraints weight = 3650.120| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8720 Z= 0.172 Angle : 0.665 8.356 11840 Z= 0.343 Chirality : 0.040 0.155 1392 Planarity : 0.005 0.042 1416 Dihedral : 7.480 57.922 1128 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.00 % Allowed : 23.62 % Favored : 71.38 % 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: -0.98 (0.25), residues: 1032 helix: -0.23 (0.18), residues: 712 sheet: -1.86 (0.80), residues: 36 loop : -1.22 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 841 TYR 0.014 0.002 TYR A 915 PHE 0.028 0.001 PHE B 831 TRP 0.009 0.001 TRP H 30 HIS 0.001 0.000 HIS D 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 8708) covalent geometry : angle 0.66548 / 0.34 (11816) SS BOND : bond 0.00195 / 0.11 ( 12) SS BOND : angle 0.39872 / 0.25 ( 24) hydrogen bonds : bond 0.04766 / 3.22 ( 573) hydrogen bonds : angle 5.42192 / 3.90 ( 1599) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 292 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 LEU cc_start: 0.9041 (mm) cc_final: 0.8778 (mm) REVERT: A 829 ARG cc_start: 0.8783 (mtp180) cc_final: 0.8225 (mmm-85) REVERT: A 840 MET cc_start: 0.6996 (mmm) cc_final: 0.6763 (mmp) REVERT: A 866 TYR cc_start: 0.9092 (t80) cc_final: 0.8842 (t80) REVERT: A 880 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8334 (p90) REVERT: A 898 MET cc_start: 0.8753 (tmm) cc_final: 0.8118 (tmm) REVERT: A 903 TRP cc_start: 0.8736 (p-90) cc_final: 0.7954 (p-90) REVERT: B 748 LEU cc_start: 0.8957 (mm) cc_final: 0.8654 (mm) REVERT: B 829 ARG cc_start: 0.8743 (mtp180) cc_final: 0.8155 (mmm-85) REVERT: B 874 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8395 (tm-30) REVERT: B 880 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8340 (p90) REVERT: C 724 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7761 (tp) REVERT: C 745 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9312 (mm) REVERT: C 748 LEU cc_start: 0.9163 (mm) cc_final: 0.8892 (mm) REVERT: C 750 MET cc_start: 0.8553 (tpt) cc_final: 0.8253 (tpt) REVERT: C 759 GLU cc_start: 0.8187 (tp30) cc_final: 0.7502 (pm20) REVERT: C 826 ARG cc_start: 0.8677 (mmm-85) cc_final: 0.8473 (mmm-85) REVERT: C 829 ARG cc_start: 0.8785 (mtp180) cc_final: 0.8136 (mmm-85) REVERT: C 840 MET cc_start: 0.7123 (mmm) cc_final: 0.6908 (mmm) REVERT: C 880 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8040 (p90) REVERT: C 898 MET cc_start: 0.8705 (tmm) cc_final: 0.8131 (tmm) REVERT: C 903 TRP cc_start: 0.8774 (p-90) cc_final: 0.7884 (p-90) REVERT: D 748 LEU cc_start: 0.9244 (mm) cc_final: 0.9018 (mm) REVERT: D 750 MET cc_start: 0.8702 (tpt) cc_final: 0.8437 (tpt) REVERT: D 759 GLU cc_start: 0.8223 (tp30) cc_final: 0.7478 (pm20) REVERT: D 829 ARG cc_start: 0.8735 (mtp180) cc_final: 0.8313 (mtp85) REVERT: D 840 MET cc_start: 0.6904 (mmm) cc_final: 0.6576 (mmp) REVERT: D 880 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8275 (p90) REVERT: D 898 MET cc_start: 0.8746 (tmm) cc_final: 0.8189 (tmm) REVERT: D 903 TRP cc_start: 0.8707 (p-90) cc_final: 0.8010 (p-90) outliers start: 47 outliers final: 27 residues processed: 319 average time/residue: 0.0813 time to fit residues: 36.2745 Evaluate side-chains 278 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 880 PHE Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 935 ASN Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 880 PHE Chi-restraints excluded: chain D residue 929 VAL Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [92, 73, 81, 88, 82, 1, 68, 78, 8, 54, 47] chunk 92 optimal weight: 30.0000 chunk 73 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 82 optimal weight: 0.0570 chunk 1 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 746 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.143257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.108928 restraints weight = 21154.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.112351 restraints weight = 9389.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.114177 restraints weight = 5907.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.115269 restraints weight = 4663.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.115609 restraints weight = 4127.283| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8720 Z= 0.238 Angle : 0.715 7.222 11840 Z= 0.373 Chirality : 0.042 0.159 1392 Planarity : 0.005 0.036 1416 Dihedral : 6.950 51.971 1126 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 6.81 % Allowed : 25.43 % Favored : 67.77 % 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: -0.63 (0.25), residues: 1032 helix: 0.01 (0.18), residues: 728 sheet: None (None), residues: 0 loop : -1.23 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 841 TYR 0.020 0.003 TYR B 915 PHE 0.027 0.002 PHE C 802 TRP 0.024 0.002 TRP G 30 HIS 0.002 0.001 HIS D 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.24 ( 8708) covalent geometry : angle 0.71502 / 0.37 (11816) SS BOND : bond 0.00190 / 0.11 ( 12) SS BOND : angle 0.37991 / 0.22 ( 24) hydrogen bonds : bond 0.04898 / 3.27 ( 573) hydrogen bonds : angle 5.54714 / 3.99 ( 1599) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 LEU cc_start: 0.9085 (mm) cc_final: 0.8553 (mm) REVERT: A 808 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7904 (mm) REVERT: A 829 ARG cc_start: 0.8753 (mtp180) cc_final: 0.8007 (mmm-85) REVERT: A 840 MET cc_start: 0.7078 (mmm) cc_final: 0.6848 (mmp) REVERT: A 866 TYR cc_start: 0.9086 (t80) cc_final: 0.8853 (t80) REVERT: A 874 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8369 (tm-30) REVERT: A 880 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8447 (p90) REVERT: A 901 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8264 (pp20) REVERT: A 903 TRP cc_start: 0.8786 (p-90) cc_final: 0.8193 (p-90) REVERT: B 748 LEU cc_start: 0.9049 (mm) cc_final: 0.8759 (mm) REVERT: B 808 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7913 (mm) REVERT: B 829 ARG cc_start: 0.8702 (mtp180) cc_final: 0.8223 (mtp85) REVERT: B 874 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8436 (tm-30) REVERT: B 880 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8419 (p90) REVERT: B 903 TRP cc_start: 0.8800 (p-90) cc_final: 0.7928 (p-90) REVERT: C 745 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9189 (mm) REVERT: C 748 LEU cc_start: 0.9248 (mm) cc_final: 0.9029 (mm) REVERT: C 750 MET cc_start: 0.8422 (tpt) cc_final: 0.8167 (tpt) REVERT: C 829 ARG cc_start: 0.8758 (mtp180) cc_final: 0.8148 (mmm-85) REVERT: C 840 MET cc_start: 0.6812 (mmm) cc_final: 0.6424 (mmp) REVERT: C 880 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8365 (p90) REVERT: C 898 MET cc_start: 0.8736 (tmm) cc_final: 0.8210 (tmm) REVERT: C 903 TRP cc_start: 0.8856 (p-90) cc_final: 0.8039 (p-90) REVERT: D 750 MET cc_start: 0.8659 (tpt) cc_final: 0.8361 (tpt) REVERT: D 829 ARG cc_start: 0.8736 (mtp180) cc_final: 0.8193 (mmm-85) REVERT: D 840 MET cc_start: 0.6999 (mmm) cc_final: 0.6585 (mmp) REVERT: D 880 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8405 (p90) REVERT: D 898 MET cc_start: 0.8770 (tmm) cc_final: 0.8270 (tmm) REVERT: D 903 TRP cc_start: 0.8793 (p-90) cc_final: 0.7919 (p-90) outliers start: 64 outliers final: 35 residues processed: 289 average time/residue: 0.0809 time to fit residues: 32.8487 Evaluate side-chains 288 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 880 PHE Chi-restraints excluded: chain B residue 935 ASN Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 800 ASP Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 871 MET Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 800 ASP Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain D residue 880 PHE Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain D residue 941 ILE Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [25, 54, 24, 22, 31, 51, 14, 96, 9, 45, 40] chunk 25 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 96 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 746 ASN B 746 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.144702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.110577 restraints weight = 20849.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.114059 restraints weight = 9349.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.116017 restraints weight = 5821.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.117062 restraints weight = 4519.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117593 restraints weight = 4008.543| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8720 Z= 0.201 Angle : 0.688 6.422 11840 Z= 0.355 Chirality : 0.041 0.177 1392 Planarity : 0.004 0.032 1416 Dihedral : 6.431 49.218 1124 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.85 % Allowed : 29.57 % Favored : 64.57 % 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: -0.35 (0.25), residues: 1032 helix: 0.21 (0.18), residues: 728 sheet: None (None), residues: 0 loop : -1.10 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 841 TYR 0.016 0.002 TYR B 915 PHE 0.031 0.002 PHE B 831 TRP 0.013 0.002 TRP E 30 HIS 0.001 0.000 HIS D 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 ( 8708) covalent geometry : angle 0.68821 / 0.36 (11816) SS BOND : bond 0.00114 / 0.07 ( 12) SS BOND : angle 0.28859 / 0.18 ( 24) hydrogen bonds : bond 0.04753 / 3.18 ( 573) hydrogen bonds : angle 5.43841 / 3.92 ( 1599) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9079 (mm) REVERT: A 748 LEU cc_start: 0.8979 (mm) cc_final: 0.8687 (mm) REVERT: A 829 ARG cc_start: 0.8739 (mtp180) cc_final: 0.8153 (mmm-85) REVERT: A 903 TRP cc_start: 0.8893 (p-90) cc_final: 0.8264 (p-90) REVERT: B 745 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9004 (mm) REVERT: B 748 LEU cc_start: 0.9065 (mm) cc_final: 0.8826 (mm) REVERT: B 874 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8408 (tm-30) REVERT: B 898 MET cc_start: 0.8856 (tmm) cc_final: 0.8362 (tmm) REVERT: B 903 TRP cc_start: 0.8847 (p-90) cc_final: 0.7988 (p-90) REVERT: C 745 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9047 (mm) REVERT: C 750 MET cc_start: 0.8370 (tpt) cc_final: 0.8102 (tpt) REVERT: C 808 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7931 (mm) REVERT: C 829 ARG cc_start: 0.8822 (mtp180) cc_final: 0.8107 (mmm-85) REVERT: C 880 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8452 (p90) REVERT: C 898 MET cc_start: 0.8786 (tmm) cc_final: 0.8250 (tmm) REVERT: C 903 TRP cc_start: 0.8846 (p-90) cc_final: 0.8066 (p-90) REVERT: D 724 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7809 (mp) REVERT: D 748 LEU cc_start: 0.9212 (mm) cc_final: 0.8869 (mm) REVERT: D 750 MET cc_start: 0.8617 (tpt) cc_final: 0.8412 (tpt) REVERT: D 829 ARG cc_start: 0.8759 (mtp180) cc_final: 0.8377 (mtp180) REVERT: D 840 MET cc_start: 0.7061 (mmm) cc_final: 0.6669 (mmp) REVERT: D 898 MET cc_start: 0.8815 (tmm) cc_final: 0.8303 (tmm) REVERT: D 903 TRP cc_start: 0.8822 (p-90) cc_final: 0.7990 (p-90) outliers start: 55 outliers final: 31 residues processed: 291 average time/residue: 0.0825 time to fit residues: 33.7585 Evaluate side-chains 287 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 880 PHE Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 941 ILE Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain D residue 941 ILE Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 2 CYS Chi-restraints excluded: chain F residue 33 TRP Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [46, 2, 83, 3, 42, 77, 28, 14, 45, 27, 47] chunk 46 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 42 optimal weight: 0.1980 chunk 77 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 746 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.146376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.112726 restraints weight = 20623.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.116216 restraints weight = 9155.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.118243 restraints weight = 5673.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.119334 restraints weight = 4380.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.119773 restraints weight = 3846.419| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8720 Z= 0.161 Angle : 0.681 8.219 11840 Z= 0.351 Chirality : 0.041 0.226 1392 Planarity : 0.004 0.034 1416 Dihedral : 6.172 55.577 1121 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.06 % Allowed : 30.11 % Favored : 63.83 % 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: -0.19 (0.26), residues: 1032 helix: 0.35 (0.18), residues: 728 sheet: None (None), residues: 0 loop : -1.08 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 841 TYR 0.026 0.002 TYR A 866 PHE 0.024 0.001 PHE B 831 TRP 0.012 0.001 TRP E 30 HIS 0.002 0.001 HIS C 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 8708) covalent geometry : angle 0.68156 / 0.35 (11816) SS BOND : bond 0.00090 / 0.06 ( 12) SS BOND : angle 0.29859 / 0.20 ( 24) hydrogen bonds : bond 0.04675 / 3.15 ( 573) hydrogen bonds : angle 5.29571 / 3.81 ( 1599) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 262 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 LEU cc_start: 0.8972 (mm) cc_final: 0.8718 (mm) REVERT: A 829 ARG cc_start: 0.8758 (mtp180) cc_final: 0.8195 (mmm-85) REVERT: A 840 MET cc_start: 0.6381 (mmp) cc_final: 0.6145 (mmp) REVERT: A 903 TRP cc_start: 0.8834 (p-90) cc_final: 0.8046 (p-90) REVERT: B 745 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9021 (mm) REVERT: B 748 LEU cc_start: 0.9079 (mm) cc_final: 0.8738 (mm) REVERT: B 808 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7955 (mm) REVERT: B 829 ARG cc_start: 0.8623 (mtp180) cc_final: 0.8285 (mtp85) REVERT: B 840 MET cc_start: 0.6951 (mmm) cc_final: 0.6749 (mmm) REVERT: B 874 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 903 TRP cc_start: 0.8829 (p-90) cc_final: 0.7977 (p-90) REVERT: C 724 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7679 (tp) REVERT: C 750 MET cc_start: 0.8352 (tpt) cc_final: 0.8081 (tpt) REVERT: C 808 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7926 (mm) REVERT: C 829 ARG cc_start: 0.8834 (mtp180) cc_final: 0.8546 (mtp180) REVERT: C 898 MET cc_start: 0.8765 (tmm) cc_final: 0.8213 (tmm) REVERT: C 903 TRP cc_start: 0.8833 (p-90) cc_final: 0.8007 (p-90) REVERT: D 724 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7715 (tp) REVERT: D 749 PHE cc_start: 0.8368 (t80) cc_final: 0.8135 (t80) REVERT: D 808 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7850 (mm) REVERT: D 829 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8381 (mtp180) REVERT: D 840 MET cc_start: 0.6999 (mmm) cc_final: 0.6685 (mmp) REVERT: D 898 MET cc_start: 0.8793 (tmm) cc_final: 0.8263 (tmm) REVERT: D 903 TRP cc_start: 0.8782 (p-90) cc_final: 0.8024 (p-90) outliers start: 57 outliers final: 33 residues processed: 296 average time/residue: 0.0763 time to fit residues: 31.7662 Evaluate side-chains 295 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 752 MET Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 2 CYS Chi-restraints excluded: chain F residue 33 TRP Chi-restraints excluded: chain G residue 2 CYS Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [36, 54, 12, 38, 31, 98, 57, 64, 20, 87, 58] chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 746 ASN B 746 ASN C 746 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.147144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113363 restraints weight = 20633.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116952 restraints weight = 9076.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119001 restraints weight = 5599.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.120071 restraints weight = 4322.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.120685 restraints weight = 3811.449| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8720 Z= 0.157 Angle : 0.715 12.112 11840 Z= 0.361 Chirality : 0.042 0.369 1392 Planarity : 0.004 0.035 1416 Dihedral : 6.080 57.992 1120 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.91 % Allowed : 29.79 % Favored : 63.30 % 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: -0.11 (0.26), residues: 1032 helix: 0.43 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.13 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 826 TYR 0.027 0.002 TYR C 866 PHE 0.037 0.001 PHE B 802 TRP 0.011 0.001 TRP E 30 HIS 0.002 0.000 HIS D 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 8708) covalent geometry : angle 0.71582 / 0.36 (11816) SS BOND : bond 0.00075 / 0.05 ( 12) SS BOND : angle 0.27317 / 0.18 ( 24) hydrogen bonds : bond 0.04590 / 3.06 ( 573) hydrogen bonds : angle 5.23170 / 3.77 ( 1599) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 271 time to evaluate : 0.327 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: A 748 LEU cc_start: 0.8991 (mm) cc_final: 0.8757 (mm) REVERT: A 829 ARG cc_start: 0.8800 (mtp180) cc_final: 0.8251 (mmm-85) REVERT: A 878 GLU cc_start: 0.8108 (pp20) cc_final: 0.7896 (pp20) REVERT: A 898 MET cc_start: 0.8772 (tmm) cc_final: 0.8251 (tmm) REVERT: A 903 TRP cc_start: 0.8804 (p-90) cc_final: 0.7924 (p-90) REVERT: B 745 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9035 (mm) REVERT: B 748 LEU cc_start: 0.8994 (mm) cc_final: 0.8766 (mm) REVERT: B 829 ARG cc_start: 0.8631 (mtp180) cc_final: 0.7718 (mmm-85) REVERT: B 874 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8298 (tm-30) REVERT: B 903 TRP cc_start: 0.8826 (p-90) cc_final: 0.7949 (p-90) REVERT: C 724 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7631 (mt) REVERT: C 750 MET cc_start: 0.8386 (tpt) cc_final: 0.8168 (tpt) REVERT: C 808 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7922 (mm) REVERT: C 829 ARG cc_start: 0.8799 (mtp180) cc_final: 0.8393 (mtp85) REVERT: C 898 MET cc_start: 0.8763 (tmm) cc_final: 0.8208 (tmm) REVERT: C 903 TRP cc_start: 0.8839 (p-90) cc_final: 0.8041 (p-90) REVERT: D 724 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7666 (mt) REVERT: D 749 PHE cc_start: 0.8431 (t80) cc_final: 0.8093 (t80) REVERT: D 808 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7830 (mm) REVERT: D 829 ARG cc_start: 0.8790 (mtp180) cc_final: 0.8405 (mtp180) REVERT: D 840 MET cc_start: 0.6948 (mmm) cc_final: 0.6643 (mmp) REVERT: D 898 MET cc_start: 0.8767 (tmm) cc_final: 0.8208 (tmm) REVERT: D 903 TRP cc_start: 0.8771 (p-90) cc_final: 0.7958 (p-90) outliers start: 65 outliers final: 40 residues processed: 308 average time/residue: 0.0787 time to fit residues: 34.1990 Evaluate side-chains 300 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 941 ILE Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 752 MET Chi-restraints excluded: chain D residue 789 ILE Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 871 MET Chi-restraints excluded: chain D residue 880 PHE Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain D residue 941 ILE Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 2 CYS Chi-restraints excluded: chain F residue 33 TRP Chi-restraints excluded: chain G residue 2 CYS Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [97, 37, 16, 64, 71, 30, 93, 43, 26, 38, 54] chunk 97 optimal weight: 20.0000 chunk 37 optimal weight: 0.2980 chunk 16 optimal weight: 7.9990 chunk 64 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 728 ASN B 746 ASN C 746 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.147871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.113846 restraints weight = 20345.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.117392 restraints weight = 8926.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.119515 restraints weight = 5421.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.120599 restraints weight = 4116.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.121227 restraints weight = 3606.891| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8720 Z= 0.150 Angle : 0.776 14.388 11840 Z= 0.381 Chirality : 0.044 0.345 1392 Planarity : 0.004 0.038 1416 Dihedral : 6.032 59.061 1120 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.85 % Allowed : 32.55 % Favored : 61.60 % 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: -0.09 (0.26), residues: 1032 helix: 0.65 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.57 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.023 0.002 TYR D 866 PHE 0.040 0.001 PHE A 802 TRP 0.013 0.001 TRP E 30 HIS 0.002 0.001 HIS B 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 8708) covalent geometry : angle 0.77694 / 0.38 (11816) SS BOND : bond 0.00074 / 0.04 ( 12) SS BOND : angle 0.36205 / 0.24 ( 24) hydrogen bonds : bond 0.04564 / 3.07 ( 573) hydrogen bonds : angle 5.12021 / 3.70 ( 1599) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 278 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 752 MET cc_start: 0.7331 (mpp) cc_final: 0.6313 (tpt) REVERT: A 829 ARG cc_start: 0.8821 (mtp180) cc_final: 0.8238 (mmm-85) REVERT: A 878 GLU cc_start: 0.7983 (pp20) cc_final: 0.7487 (pp20) REVERT: A 898 MET cc_start: 0.8812 (tmm) cc_final: 0.8272 (tmm) REVERT: A 903 TRP cc_start: 0.8825 (p-90) cc_final: 0.8006 (p-90) REVERT: B 724 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7846 (tp) REVERT: B 745 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9056 (mm) REVERT: B 748 LEU cc_start: 0.9065 (mm) cc_final: 0.8739 (mm) REVERT: B 752 MET cc_start: 0.8342 (ptp) cc_final: 0.7086 (mmt) REVERT: B 808 LEU cc_start: 0.8809 (mm) cc_final: 0.8530 (mm) REVERT: B 829 ARG cc_start: 0.8678 (mtp180) cc_final: 0.7762 (mmm-85) REVERT: B 903 TRP cc_start: 0.8830 (p-90) cc_final: 0.7898 (p-90) REVERT: C 724 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7687 (mt) REVERT: C 749 PHE cc_start: 0.8574 (t80) cc_final: 0.8318 (t80) REVERT: C 750 MET cc_start: 0.8432 (tpt) cc_final: 0.8000 (tpt) REVERT: C 898 MET cc_start: 0.8759 (tmm) cc_final: 0.8195 (tmm) REVERT: C 903 TRP cc_start: 0.8849 (p-90) cc_final: 0.8056 (p-90) REVERT: D 724 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7754 (mt) REVERT: D 749 PHE cc_start: 0.8464 (t80) cc_final: 0.8063 (t80) REVERT: D 808 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7873 (mm) REVERT: D 829 ARG cc_start: 0.8842 (mtp180) cc_final: 0.8039 (mmm-85) REVERT: D 840 MET cc_start: 0.7064 (mmm) cc_final: 0.6742 (mmp) REVERT: D 898 MET cc_start: 0.8762 (tmm) cc_final: 0.8167 (tmm) REVERT: D 903 TRP cc_start: 0.8731 (p-90) cc_final: 0.7942 (p-90) outliers start: 55 outliers final: 30 residues processed: 311 average time/residue: 0.0820 time to fit residues: 35.8493 Evaluate side-chains 291 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 931 PHE Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 722 MET Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 752 MET Chi-restraints excluded: chain D residue 789 ILE Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 911 LEU Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain D residue 941 ILE Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 33 TRP Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [13, 9, 56, 77, 5, 4, 27, 63, 15, 62, 25] chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 746 ASN C 728 ASN D 728 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.144782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110094 restraints weight = 20352.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.113448 restraints weight = 9183.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.115383 restraints weight = 5673.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.116452 restraints weight = 4374.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.116875 restraints weight = 3842.047| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8720 Z= 0.196 Angle : 0.803 13.783 11840 Z= 0.399 Chirality : 0.046 0.412 1392 Planarity : 0.004 0.036 1416 Dihedral : 6.116 59.982 1120 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.74 % Allowed : 33.62 % Favored : 60.64 % 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: -0.30 (0.26), residues: 1032 helix: 0.32 (0.19), residues: 728 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 841 TYR 0.015 0.002 TYR A 723 PHE 0.027 0.001 PHE B 802 TRP 0.012 0.001 TRP H 30 HIS 0.002 0.000 HIS C 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 ( 8708) covalent geometry : angle 0.80421 / 0.40 (11816) SS BOND : bond 0.00063 / 0.04 ( 12) SS BOND : angle 0.22395 / 0.14 ( 24) hydrogen bonds : bond 0.04469 / 3.00 ( 573) hydrogen bonds : angle 5.29542 / 3.83 ( 1599) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 752 MET cc_start: 0.7433 (mpp) cc_final: 0.6400 (tpt) REVERT: A 829 ARG cc_start: 0.8846 (mtp180) cc_final: 0.8285 (mmm-85) REVERT: A 903 TRP cc_start: 0.8872 (p-90) cc_final: 0.8134 (p-90) REVERT: B 745 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8982 (mm) REVERT: B 748 LEU cc_start: 0.9046 (mm) cc_final: 0.8739 (mm) REVERT: B 752 MET cc_start: 0.8398 (ptp) cc_final: 0.7175 (tpt) REVERT: B 829 ARG cc_start: 0.8666 (mtp180) cc_final: 0.7803 (mmm-85) REVERT: B 903 TRP cc_start: 0.8892 (p-90) cc_final: 0.7994 (p-90) REVERT: C 724 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7735 (mt) REVERT: C 826 ARG cc_start: 0.8832 (mmm-85) cc_final: 0.8444 (ttm110) REVERT: C 829 ARG cc_start: 0.8696 (mtp180) cc_final: 0.8471 (mtp85) REVERT: D 724 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7732 (mt) REVERT: D 808 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7857 (mm) REVERT: D 829 ARG cc_start: 0.8812 (mtp180) cc_final: 0.8059 (mmm-85) REVERT: D 898 MET cc_start: 0.8790 (tmm) cc_final: 0.8241 (tmm) REVERT: D 903 TRP cc_start: 0.8802 (p-90) cc_final: 0.7966 (p-90) outliers start: 54 outliers final: 35 residues processed: 289 average time/residue: 0.0784 time to fit residues: 32.0972 Evaluate side-chains 291 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 931 PHE Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 728 ASN Chi-restraints excluded: chain D residue 789 ILE Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 2 CYS Chi-restraints excluded: chain F residue 33 TRP Chi-restraints excluded: chain G residue 2 CYS Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [21, 72, 36, 81, 6, 48, 63, 66, 25, 39, 93] chunk 21 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 66 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 746 ASN C 728 ASN D 728 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.145856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.111474 restraints weight = 20317.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.114833 restraints weight = 9099.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.116851 restraints weight = 5608.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.117859 restraints weight = 4292.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.118312 restraints weight = 3778.103| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8720 Z= 0.183 Angle : 0.837 14.073 11840 Z= 0.411 Chirality : 0.046 0.390 1392 Planarity : 0.004 0.036 1416 Dihedral : 6.178 58.969 1120 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.94 % Allowed : 35.53 % Favored : 60.53 % 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: -0.38 (0.26), residues: 1032 helix: 0.26 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.25 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 841 TYR 0.015 0.002 TYR B 866 PHE 0.035 0.002 PHE A 802 TRP 0.011 0.001 TRP H 30 HIS 0.001 0.000 HIS B 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 8708) covalent geometry : angle 0.83815 / 0.41 (11816) SS BOND : bond 0.00068 / 0.04 ( 12) SS BOND : angle 0.21938 / 0.13 ( 24) hydrogen bonds : bond 0.04558 / 3.05 ( 573) hydrogen bonds : angle 5.28319 / 3.82 ( 1599) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 752 MET cc_start: 0.7369 (mpp) cc_final: 0.6303 (tpt) REVERT: A 829 ARG cc_start: 0.8791 (mtp180) cc_final: 0.8225 (mmm-85) REVERT: A 898 MET cc_start: 0.8752 (tmm) cc_final: 0.8238 (tmm) REVERT: A 903 TRP cc_start: 0.8836 (p-90) cc_final: 0.8089 (p-90) REVERT: B 745 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8988 (mm) REVERT: B 748 LEU cc_start: 0.9029 (mm) cc_final: 0.8731 (mm) REVERT: B 752 MET cc_start: 0.8276 (ptp) cc_final: 0.7082 (tpt) REVERT: B 829 ARG cc_start: 0.8672 (mtp180) cc_final: 0.7806 (mmm-85) REVERT: B 903 TRP cc_start: 0.8864 (p-90) cc_final: 0.7980 (p-90) REVERT: C 749 PHE cc_start: 0.8458 (t80) cc_final: 0.8080 (t80) REVERT: C 826 ARG cc_start: 0.8820 (mmm-85) cc_final: 0.8421 (ttm110) REVERT: C 829 ARG cc_start: 0.8698 (mtp180) cc_final: 0.8482 (mtp85) REVERT: C 898 MET cc_start: 0.8759 (tmm) cc_final: 0.8230 (tmm) REVERT: D 749 PHE cc_start: 0.8470 (t80) cc_final: 0.8005 (t80) REVERT: D 808 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7855 (mm) REVERT: D 829 ARG cc_start: 0.8807 (mtp180) cc_final: 0.8060 (mmm-85) REVERT: D 840 MET cc_start: 0.6434 (mmm) cc_final: 0.6066 (mmp) REVERT: D 898 MET cc_start: 0.8753 (tmm) cc_final: 0.8193 (tmm) REVERT: D 903 TRP cc_start: 0.8736 (p-90) cc_final: 0.7941 (p-90) outliers start: 37 outliers final: 32 residues processed: 273 average time/residue: 0.0814 time to fit residues: 31.1057 Evaluate side-chains 286 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 931 PHE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 931 PHE Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain D residue 789 ILE Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain F residue 2 CYS Chi-restraints excluded: chain F residue 33 TRP Chi-restraints excluded: chain G residue 2 CYS Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain H residue 2 CYS Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 33 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [26, 9, 11, 78, 96, 7, 44, 43, 84, 66, 46] chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 84 optimal weight: 0.3980 chunk 66 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 746 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.143685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.109793 restraints weight = 20826.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.113114 restraints weight = 9439.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.115027 restraints weight = 5909.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.116047 restraints weight = 4575.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.116502 restraints weight = 4034.811| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8720 Z= 0.254 Angle : 0.859 12.380 11840 Z= 0.435 Chirality : 0.047 0.341 1392 Planarity : 0.005 0.036 1416 Dihedral : 6.281 55.411 1120 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.47 % Allowed : 35.43 % Favored : 60.11 % 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: -0.69 (0.25), residues: 1032 helix: 0.02 (0.18), residues: 716 sheet: None (None), residues: 0 loop : -1.34 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 841 TYR 0.017 0.003 TYR D 785 PHE 0.025 0.002 PHE B 802 TRP 0.010 0.002 TRP H 30 HIS 0.002 0.000 HIS B 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 ( 8708) covalent geometry : angle 0.85955 / 0.43 (11816) SS BOND : bond 0.00147 / 0.09 ( 12) SS BOND : angle 0.31386 / 0.21 ( 24) hydrogen bonds : bond 0.04674 / 3.14 ( 573) hydrogen bonds : angle 5.55288 / 4.00 ( 1599) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1739.36 seconds wall clock time: 30 minutes 32.83 seconds (1832.83 seconds total)