Starting phenix.real_space_refine on Wed Feb 4 09:08:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wzd_66391/02_2026/9wzd_66391.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wzd_66391/02_2026/9wzd_66391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wzd_66391/02_2026/9wzd_66391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wzd_66391/02_2026/9wzd_66391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wzd_66391/02_2026/9wzd_66391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wzd_66391/02_2026/9wzd_66391.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.021 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 56 5.16 5 C 6230 2.51 5 N 1708 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9870 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "D" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "G" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "H" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "J" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "L" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "M" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "N" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Time building chain proxies: 2.21, per 1000 atoms: 0.22 Number of scatterers: 9870 At special positions: 0 Unit cell: (98.28, 94.08, 98.28, 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 56 16.00 O 1876 8.00 N 1708 7.00 C 6230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.67 Conformation dependent library (CDL) restraints added in 316.0 milliseconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 0 sheets defined 79.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.830A pdb=" N LEU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 27 removed outlier: 3.866A pdb=" N LYS A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 61 through 76 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.959A pdb=" N ALA A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.733A pdb=" N LEU B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 27 removed outlier: 3.789A pdb=" N LYS B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 61 through 76 Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.786A pdb=" N ALA B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 13 removed outlier: 3.786A pdb=" N LEU C 9 " --> pdb=" O ARG C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.510A pdb=" N LYS C 21 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 61 through 76 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.807A pdb=" N ALA C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.786A pdb=" N LEU D 9 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.728A pdb=" N LYS D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 61 through 76 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.866A pdb=" N ALA D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.598A pdb=" N LEU E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 27 removed outlier: 3.751A pdb=" N LYS E 21 " --> pdb=" O ALA E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.640A pdb=" N LEU E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 60 Processing helix chain 'E' and resid 61 through 76 Processing helix chain 'E' and resid 78 through 91 removed outlier: 3.845A pdb=" N ALA E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 13 removed outlier: 3.512A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU F 9 " --> pdb=" O ARG F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 27 removed outlier: 3.888A pdb=" N LYS F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 61 through 76 Processing helix chain 'F' and resid 78 through 91 removed outlier: 3.978A pdb=" N ALA F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 13 removed outlier: 3.812A pdb=" N LEU G 9 " --> pdb=" O ARG G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 removed outlier: 3.569A pdb=" N LYS G 21 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 48 through 60 Processing helix chain 'G' and resid 61 through 76 Processing helix chain 'G' and resid 78 through 91 removed outlier: 3.902A pdb=" N ALA G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 13 removed outlier: 3.599A pdb=" N LEU H 9 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 27 removed outlier: 3.569A pdb=" N LYS H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 48 through 60 Processing helix chain 'H' and resid 61 through 76 Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'I' and resid 3 through 13 removed outlier: 3.550A pdb=" N ALA I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU I 9 " --> pdb=" O ARG I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 27 removed outlier: 3.661A pdb=" N LYS I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 48 through 60 Processing helix chain 'I' and resid 61 through 76 Processing helix chain 'I' and resid 78 through 91 removed outlier: 3.647A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 14 removed outlier: 3.650A pdb=" N ASN J 14 " --> pdb=" O ASP J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 3.530A pdb=" N LYS J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 48 through 60 Processing helix chain 'J' and resid 61 through 76 Processing helix chain 'J' and resid 78 through 91 removed outlier: 3.744A pdb=" N ALA J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 14 removed outlier: 3.616A pdb=" N LEU K 9 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN K 14 " --> pdb=" O ASP K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 27 removed outlier: 3.549A pdb=" N LYS K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 61 through 76 Processing helix chain 'K' and resid 78 through 91 removed outlier: 3.860A pdb=" N ALA K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 13 Processing helix chain 'L' and resid 16 through 27 removed outlier: 3.893A pdb=" N LYS L 21 " --> pdb=" O ALA L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 48 through 60 Processing helix chain 'L' and resid 61 through 76 Processing helix chain 'L' and resid 78 through 91 removed outlier: 3.850A pdb=" N ALA L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 13 removed outlier: 3.579A pdb=" N ALA M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU M 9 " --> pdb=" O ARG M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 27 removed outlier: 3.830A pdb=" N LYS M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 45 Processing helix chain 'M' and resid 48 through 60 Processing helix chain 'M' and resid 61 through 76 Processing helix chain 'M' and resid 78 through 91 removed outlier: 3.848A pdb=" N ALA M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN M 91 " --> pdb=" O ALA M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.763A pdb=" N ALA N 7 " --> pdb=" O ARG N 3 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE N 8 " --> pdb=" O ALA N 4 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU N 9 " --> pdb=" O ARG N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 27 removed outlier: 3.643A pdb=" N LYS N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 45 Processing helix chain 'N' and resid 48 through 60 Processing helix chain 'N' and resid 61 through 76 Processing helix chain 'N' and resid 78 through 91 removed outlier: 3.888A pdb=" N ALA N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY N 83 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1824 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: 1.10 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3346 1.34 - 1.46: 1257 1.46 - 1.57: 5253 1.57 - 1.69: 0 1.69 - 1.80: 112 Bond restraints: 9968 Sorted by residual: bond pdb=" CG GLU A 80 " pdb=" CD GLU A 80 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" CB GLU A 80 " pdb=" CG GLU A 80 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" C TYR J 60 " pdb=" N LEU J 61 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.47e-02 4.63e+03 7.84e-01 bond pdb=" C TYR C 60 " pdb=" N LEU C 61 " ideal model delta sigma weight residual 1.330 1.319 0.012 1.37e-02 5.33e+03 7.43e-01 bond pdb=" CB MET J 81 " pdb=" CG MET J 81 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.15e-01 ... (remaining 9963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 13016 1.45 - 2.89: 350 2.89 - 4.34: 22 4.34 - 5.78: 5 5.78 - 7.23: 5 Bond angle restraints: 13398 Sorted by residual: angle pdb=" C MET E 76 " pdb=" N GLY E 77 " pdb=" CA GLY E 77 " ideal model delta sigma weight residual 123.44 120.69 2.75 1.19e+00 7.06e-01 5.35e+00 angle pdb=" C MET K 76 " pdb=" N GLY K 77 " pdb=" CA GLY K 77 " ideal model delta sigma weight residual 123.30 120.85 2.45 1.06e+00 8.90e-01 5.34e+00 angle pdb=" C MET M 76 " pdb=" N GLY M 77 " pdb=" CA GLY M 77 " ideal model delta sigma weight residual 123.44 120.71 2.73 1.19e+00 7.06e-01 5.26e+00 angle pdb=" N GLY K 77 " pdb=" CA GLY K 77 " pdb=" C GLY K 77 " ideal model delta sigma weight residual 113.58 116.03 -2.45 1.07e+00 8.73e-01 5.24e+00 angle pdb=" CG ARG L 33 " pdb=" CD ARG L 33 " pdb=" NE ARG L 33 " ideal model delta sigma weight residual 112.00 117.03 -5.03 2.20e+00 2.07e-01 5.22e+00 ... (remaining 13393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5681 17.99 - 35.97: 395 35.97 - 53.96: 70 53.96 - 71.94: 25 71.94 - 89.93: 3 Dihedral angle restraints: 6174 sinusoidal: 2520 harmonic: 3654 Sorted by residual: dihedral pdb=" CA ASP F 51 " pdb=" CB ASP F 51 " pdb=" CG ASP F 51 " pdb=" OD1 ASP F 51 " ideal model delta sinusoidal sigma weight residual -30.00 -87.02 57.02 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU D 80 " pdb=" CG GLU D 80 " pdb=" CD GLU D 80 " pdb=" OE1 GLU D 80 " ideal model delta sinusoidal sigma weight residual 0.00 89.93 -89.93 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CG ARG M 5 " pdb=" CD ARG M 5 " pdb=" NE ARG M 5 " pdb=" CZ ARG M 5 " ideal model delta sinusoidal sigma weight residual -180.00 -137.18 -42.82 2 1.50e+01 4.44e-03 9.86e+00 ... (remaining 6171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 863 0.025 - 0.050: 454 0.050 - 0.075: 178 0.075 - 0.100: 41 0.100 - 0.125: 32 Chirality restraints: 1568 Sorted by residual: chirality pdb=" CA ILE H 39 " pdb=" N ILE H 39 " pdb=" C ILE H 39 " pdb=" CB ILE H 39 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE M 39 " pdb=" N ILE M 39 " pdb=" C ILE M 39 " pdb=" CB ILE M 39 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE A 39 " pdb=" N ILE A 39 " pdb=" C ILE A 39 " pdb=" CB ILE A 39 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 1565 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG M 74 " 0.153 9.50e-02 1.11e+02 6.85e-02 2.92e+00 pdb=" NE ARG M 74 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG M 74 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG M 74 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG M 74 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 33 " 0.109 9.50e-02 1.11e+02 4.88e-02 1.69e+00 pdb=" NE ARG L 33 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG L 33 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG L 33 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG L 33 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 59 " -0.010 2.00e-02 2.50e+03 9.14e-03 1.46e+00 pdb=" CG PHE I 59 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE I 59 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE I 59 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE I 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 59 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE I 59 " -0.002 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 276 2.71 - 3.26: 9720 3.26 - 3.80: 15024 3.80 - 4.35: 19246 4.35 - 4.90: 32323 Nonbonded interactions: 76589 Sorted by model distance: nonbonded pdb=" NH2 ARG H 74 " pdb=" OE1 GLN H 86 " model vdw 2.161 3.120 nonbonded pdb=" NH2 ARG A 74 " pdb=" OE1 GLN A 86 " model vdw 2.161 3.120 nonbonded pdb=" OD1 ASN L 71 " pdb=" NH2 ARG L 74 " model vdw 2.193 3.120 nonbonded pdb=" OG1 THR L 16 " pdb=" OE1 GLU L 19 " model vdw 2.207 3.040 nonbonded pdb=" O GLY B 35 " pdb=" NE2 GLN N 79 " model vdw 2.218 3.120 ... (remaining 76584 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.560 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 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 : 0.004 0.030 9968 Z= 0.191 Angle : 0.549 7.230 13398 Z= 0.308 Chirality : 0.037 0.125 1568 Planarity : 0.004 0.069 1722 Dihedral : 12.923 89.931 3822 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.99 (0.25), residues: 1246 helix: 0.61 (0.18), residues: 896 sheet: None (None), residues: 0 loop : 1.24 (0.37), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 33 TYR 0.012 0.002 TYR D 60 PHE 0.021 0.002 PHE I 59 HIS 0.003 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9968) covalent geometry : angle 0.54920 (13398) hydrogen bonds : bond 0.17206 ( 608) hydrogen bonds : angle 6.49749 ( 1824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.8370 (ptt-90) cc_final: 0.8152 (pmm-80) REVERT: A 18 GLU cc_start: 0.8581 (tp30) cc_final: 0.8331 (tp30) REVERT: B 18 GLU cc_start: 0.8508 (tp30) cc_final: 0.8251 (tp30) REVERT: B 75 ASP cc_start: 0.8493 (t70) cc_final: 0.8088 (t0) REVERT: C 75 ASP cc_start: 0.8363 (t0) cc_final: 0.8097 (t0) REVERT: E 18 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8010 (tm-30) REVERT: E 48 ASP cc_start: 0.8597 (p0) cc_final: 0.8261 (p0) REVERT: E 75 ASP cc_start: 0.8499 (t70) cc_final: 0.8070 (t70) REVERT: F 18 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8417 (tm-30) REVERT: F 75 ASP cc_start: 0.8738 (t0) cc_final: 0.8503 (t0) REVERT: G 75 ASP cc_start: 0.8580 (t0) cc_final: 0.8251 (t0) REVERT: H 1 MET cc_start: 0.6937 (tpt) cc_final: 0.6707 (tpt) REVERT: I 10 ASP cc_start: 0.8998 (m-30) cc_final: 0.8777 (m-30) REVERT: I 18 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8294 (tm-30) REVERT: I 48 ASP cc_start: 0.8180 (p0) cc_final: 0.7949 (p0) REVERT: I 51 ASP cc_start: 0.8879 (m-30) cc_final: 0.8513 (m-30) REVERT: I 62 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7606 (mt-10) REVERT: I 75 ASP cc_start: 0.8700 (t70) cc_final: 0.8457 (OUTLIER) REVERT: J 3 ARG cc_start: 0.2863 (mmt180) cc_final: 0.2346 (mmt180) REVERT: J 6 ASP cc_start: 0.9163 (m-30) cc_final: 0.8543 (m-30) REVERT: J 48 ASP cc_start: 0.8518 (p0) cc_final: 0.8106 (p0) REVERT: J 51 ASP cc_start: 0.9069 (m-30) cc_final: 0.8830 (m-30) REVERT: J 75 ASP cc_start: 0.8774 (t70) cc_final: 0.8424 (t0) REVERT: K 26 LYS cc_start: 0.9366 (mmmm) cc_final: 0.9129 (mmtp) REVERT: K 51 ASP cc_start: 0.9004 (m-30) cc_final: 0.8656 (m-30) REVERT: L 26 LYS cc_start: 0.9366 (mmmm) cc_final: 0.9008 (mmmt) REVERT: L 75 ASP cc_start: 0.8624 (t0) cc_final: 0.8355 (t0) REVERT: M 51 ASP cc_start: 0.8883 (m-30) cc_final: 0.8679 (m-30) REVERT: N 10 ASP cc_start: 0.8778 (m-30) cc_final: 0.8490 (m-30) REVERT: N 18 GLU cc_start: 0.8365 (tp30) cc_final: 0.8165 (tp30) REVERT: N 48 ASP cc_start: 0.8385 (p0) cc_final: 0.8171 (p0) REVERT: N 75 ASP cc_start: 0.8697 (t70) cc_final: 0.8302 (t0) outliers start: 0 outliers final: 1 residues processed: 408 average time/residue: 0.6700 time to fit residues: 286.7721 Evaluate side-chains 360 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 84 GLN C 71 ASN D 79 GLN E 84 GLN G 79 GLN H 71 ASN H 84 GLN J 71 ASN J 84 GLN J 86 GLN K 79 GLN K 84 GLN K 86 GLN L 84 GLN M 71 ASN M 86 GLN N 14 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.070374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.056975 restraints weight = 19974.971| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 3.12 r_work: 0.2507 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9968 Z= 0.125 Angle : 0.479 5.782 13398 Z= 0.254 Chirality : 0.036 0.135 1568 Planarity : 0.003 0.026 1722 Dihedral : 3.476 14.439 1386 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.35 % Allowed : 17.61 % Favored : 80.04 % 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: 1.11 (0.25), residues: 1246 helix: 0.76 (0.18), residues: 910 sheet: None (None), residues: 0 loop : 1.09 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 41 TYR 0.009 0.001 TYR D 60 PHE 0.010 0.002 PHE B 59 HIS 0.001 0.000 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9968) covalent geometry : angle 0.47883 (13398) hydrogen bonds : bond 0.03537 ( 608) hydrogen bonds : angle 4.52182 ( 1824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 389 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.5231 (mm-30) cc_final: 0.5018 (mm-30) REVERT: B 1 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6860 (tpp) REVERT: B 18 GLU cc_start: 0.8943 (tp30) cc_final: 0.8561 (tp30) REVERT: B 75 ASP cc_start: 0.8945 (t70) cc_final: 0.8606 (t0) REVERT: C 74 ARG cc_start: 0.8930 (mtm-85) cc_final: 0.8565 (mtm-85) REVERT: C 75 ASP cc_start: 0.8661 (t0) cc_final: 0.8375 (t0) REVERT: D 19 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8900 (mt-10) REVERT: D 81 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8099 (mtm) REVERT: E 19 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8905 (mt-10) REVERT: E 75 ASP cc_start: 0.8790 (t70) cc_final: 0.8255 (t0) REVERT: F 62 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8219 (mm-30) REVERT: F 75 ASP cc_start: 0.9074 (t0) cc_final: 0.8786 (t0) REVERT: G 3 ARG cc_start: 0.8185 (ptt180) cc_final: 0.7775 (mmm-85) REVERT: G 75 ASP cc_start: 0.8804 (t0) cc_final: 0.8511 (t0) REVERT: I 1 MET cc_start: 0.6335 (tpt) cc_final: 0.6012 (tpt) REVERT: I 18 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8408 (tm-30) REVERT: I 48 ASP cc_start: 0.8364 (p0) cc_final: 0.8134 (p0) REVERT: I 51 ASP cc_start: 0.9176 (m-30) cc_final: 0.8773 (m-30) REVERT: I 75 ASP cc_start: 0.9040 (t70) cc_final: 0.8801 (OUTLIER) REVERT: J 51 ASP cc_start: 0.9287 (m-30) cc_final: 0.9010 (m-30) REVERT: J 75 ASP cc_start: 0.9085 (t70) cc_final: 0.8706 (t0) REVERT: K 51 ASP cc_start: 0.9151 (m-30) cc_final: 0.8718 (m-30) REVERT: K 75 ASP cc_start: 0.8932 (t0) cc_final: 0.8608 (t0) REVERT: K 80 GLU cc_start: 0.4857 (pm20) cc_final: 0.4355 (pm20) REVERT: L 19 GLU cc_start: 0.8706 (pm20) cc_final: 0.8043 (pm20) REVERT: L 75 ASP cc_start: 0.9026 (t0) cc_final: 0.8716 (t0) REVERT: M 48 ASP cc_start: 0.8742 (p0) cc_final: 0.8476 (p0) REVERT: M 51 ASP cc_start: 0.9157 (m-30) cc_final: 0.8909 (m-30) REVERT: M 76 MET cc_start: 0.9246 (ptm) cc_final: 0.9016 (ptm) REVERT: N 3 ARG cc_start: 0.2113 (mmt180) cc_final: 0.1872 (mmt180) REVERT: N 6 ASP cc_start: 0.8915 (m-30) cc_final: 0.8661 (m-30) REVERT: N 10 ASP cc_start: 0.8900 (m-30) cc_final: 0.8661 (m-30) REVERT: N 18 GLU cc_start: 0.8973 (tp30) cc_final: 0.8713 (tp30) REVERT: N 75 ASP cc_start: 0.9004 (t70) cc_final: 0.8711 (t0) outliers start: 24 outliers final: 7 residues processed: 393 average time/residue: 0.6636 time to fit residues: 273.8114 Evaluate side-chains 370 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 362 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain K residue 86 GLN Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain M residue 29 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 84 GLN C 86 GLN E 84 GLN G 79 GLN H 84 GLN K 84 GLN K 86 GLN L 84 GLN L 86 GLN M 86 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.069760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.056522 restraints weight = 19826.387| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.14 r_work: 0.2510 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9968 Z= 0.125 Angle : 0.466 6.239 13398 Z= 0.244 Chirality : 0.035 0.134 1568 Planarity : 0.003 0.024 1722 Dihedral : 3.321 15.480 1386 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.94 % Allowed : 21.72 % Favored : 75.34 % 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: 1.23 (0.25), residues: 1246 helix: 0.88 (0.18), residues: 910 sheet: None (None), residues: 0 loop : 1.04 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 74 TYR 0.008 0.001 TYR A 60 PHE 0.009 0.002 PHE B 59 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9968) covalent geometry : angle 0.46563 (13398) hydrogen bonds : bond 0.03367 ( 608) hydrogen bonds : angle 4.18301 ( 1824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 378 time to evaluate : 0.413 Fit side-chains REVERT: A 33 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8379 (mtm-85) REVERT: B 1 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6665 (tpt) REVERT: B 18 GLU cc_start: 0.9005 (tp30) cc_final: 0.8620 (tp30) REVERT: B 48 ASP cc_start: 0.8396 (p0) cc_final: 0.7772 (p0) REVERT: B 51 ASP cc_start: 0.9042 (m-30) cc_final: 0.8667 (m-30) REVERT: B 75 ASP cc_start: 0.8957 (t70) cc_final: 0.8600 (t0) REVERT: C 75 ASP cc_start: 0.8657 (t0) cc_final: 0.8354 (t0) REVERT: C 81 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8337 (mtm) REVERT: C 86 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: D 19 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8630 (mt-10) REVERT: D 81 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8063 (mtm) REVERT: D 86 GLN cc_start: 0.8513 (mm110) cc_final: 0.8231 (mt0) REVERT: E 19 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8829 (mt-10) REVERT: E 75 ASP cc_start: 0.8831 (t70) cc_final: 0.8378 (t0) REVERT: F 75 ASP cc_start: 0.9126 (t0) cc_final: 0.8827 (t0) REVERT: F 80 GLU cc_start: 0.5462 (mm-30) cc_final: 0.5224 (mm-30) REVERT: G 3 ARG cc_start: 0.8161 (ptt180) cc_final: 0.7699 (mmm-85) REVERT: G 48 ASP cc_start: 0.8473 (p0) cc_final: 0.7705 (p0) REVERT: G 51 ASP cc_start: 0.9033 (m-30) cc_final: 0.8441 (m-30) REVERT: G 75 ASP cc_start: 0.8922 (t0) cc_final: 0.8597 (t0) REVERT: I 1 MET cc_start: 0.5889 (tpt) cc_final: 0.5673 (tpt) REVERT: I 18 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8243 (tm-30) REVERT: I 51 ASP cc_start: 0.9097 (m-30) cc_final: 0.8783 (m-30) REVERT: I 75 ASP cc_start: 0.9078 (t70) cc_final: 0.8857 (OUTLIER) REVERT: J 18 GLU cc_start: 0.8857 (tp30) cc_final: 0.8615 (tp30) REVERT: J 48 ASP cc_start: 0.8501 (p0) cc_final: 0.7984 (p0) REVERT: J 51 ASP cc_start: 0.9252 (m-30) cc_final: 0.8957 (m-30) REVERT: J 75 ASP cc_start: 0.9123 (t70) cc_final: 0.8775 (t0) REVERT: K 62 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: K 75 ASP cc_start: 0.9056 (t0) cc_final: 0.8838 (t70) REVERT: L 3 ARG cc_start: 0.8437 (pmt170) cc_final: 0.8071 (pmm-80) REVERT: L 19 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: L 51 ASP cc_start: 0.9089 (m-30) cc_final: 0.8856 (m-30) REVERT: L 75 ASP cc_start: 0.9083 (t0) cc_final: 0.8715 (t0) REVERT: M 21 LYS cc_start: 0.9101 (tttt) cc_final: 0.8846 (tttt) REVERT: M 48 ASP cc_start: 0.8551 (p0) cc_final: 0.8286 (p0) REVERT: M 51 ASP cc_start: 0.9124 (m-30) cc_final: 0.8864 (m-30) REVERT: M 76 MET cc_start: 0.9130 (ptm) cc_final: 0.8926 (ptm) REVERT: N 6 ASP cc_start: 0.8873 (m-30) cc_final: 0.8656 (m-30) REVERT: N 10 ASP cc_start: 0.8860 (m-30) cc_final: 0.8641 (m-30) REVERT: N 18 GLU cc_start: 0.9048 (tp30) cc_final: 0.8688 (tp30) REVERT: N 75 ASP cc_start: 0.9065 (t70) cc_final: 0.8744 (t0) outliers start: 30 outliers final: 8 residues processed: 383 average time/residue: 0.6775 time to fit residues: 272.5407 Evaluate side-chains 375 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 362 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 86 GLN Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 19 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN E 84 GLN K 14 ASN K 79 GLN K 84 GLN K 86 GLN L 84 GLN L 86 GLN M 86 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.068049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.054723 restraints weight = 19974.468| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 3.17 r_work: 0.2469 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9968 Z= 0.162 Angle : 0.487 6.777 13398 Z= 0.254 Chirality : 0.036 0.132 1568 Planarity : 0.003 0.025 1722 Dihedral : 3.321 12.820 1386 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.01 % Allowed : 23.09 % Favored : 72.90 % 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: 1.42 (0.25), residues: 1246 helix: 1.04 (0.18), residues: 910 sheet: None (None), residues: 0 loop : 1.04 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 74 TYR 0.009 0.001 TYR D 64 PHE 0.014 0.002 PHE B 59 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9968) covalent geometry : angle 0.48739 (13398) hydrogen bonds : bond 0.03622 ( 608) hydrogen bonds : angle 4.07632 ( 1824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 366 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: B 1 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6697 (tpt) REVERT: B 18 GLU cc_start: 0.9031 (tp30) cc_final: 0.8655 (tp30) REVERT: B 48 ASP cc_start: 0.8366 (p0) cc_final: 0.7771 (p0) REVERT: B 51 ASP cc_start: 0.9055 (m-30) cc_final: 0.8701 (m-30) REVERT: B 75 ASP cc_start: 0.8988 (t70) cc_final: 0.8639 (t0) REVERT: C 75 ASP cc_start: 0.8647 (t0) cc_final: 0.8356 (t0) REVERT: C 86 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: D 19 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8744 (mt-10) REVERT: D 81 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8075 (mtm) REVERT: D 86 GLN cc_start: 0.8407 (mm110) cc_final: 0.8155 (mt0) REVERT: E 19 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8759 (mt-10) REVERT: E 75 ASP cc_start: 0.8834 (t70) cc_final: 0.8356 (t0) REVERT: F 3 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8303 (ptt90) REVERT: F 62 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: F 75 ASP cc_start: 0.9097 (t0) cc_final: 0.8779 (t0) REVERT: F 80 GLU cc_start: 0.5527 (mm-30) cc_final: 0.5161 (mm-30) REVERT: G 1 MET cc_start: 0.7199 (tpp) cc_final: 0.6108 (tmm) REVERT: G 3 ARG cc_start: 0.8163 (ptt180) cc_final: 0.7646 (mmm-85) REVERT: G 75 ASP cc_start: 0.8945 (t0) cc_final: 0.8617 (t0) REVERT: H 18 GLU cc_start: 0.9158 (tp30) cc_final: 0.8818 (tp30) REVERT: I 18 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8240 (tm-30) REVERT: I 19 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8696 (pt0) REVERT: I 48 ASP cc_start: 0.8517 (p0) cc_final: 0.8195 (p0) REVERT: I 51 ASP cc_start: 0.9189 (m-30) cc_final: 0.8818 (m-30) REVERT: I 75 ASP cc_start: 0.9076 (t70) cc_final: 0.8860 (OUTLIER) REVERT: J 48 ASP cc_start: 0.8519 (p0) cc_final: 0.8054 (p0) REVERT: J 51 ASP cc_start: 0.9259 (m-30) cc_final: 0.8928 (m-30) REVERT: J 75 ASP cc_start: 0.9161 (t70) cc_final: 0.8827 (t0) REVERT: K 51 ASP cc_start: 0.9014 (m-30) cc_final: 0.8775 (m-30) REVERT: K 62 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: K 75 ASP cc_start: 0.9141 (t0) cc_final: 0.8940 (t70) REVERT: L 19 GLU cc_start: 0.8692 (pm20) cc_final: 0.8347 (pm20) REVERT: L 75 ASP cc_start: 0.9109 (t0) cc_final: 0.8749 (t0) REVERT: N 10 ASP cc_start: 0.8865 (m-30) cc_final: 0.8588 (m-30) REVERT: N 18 GLU cc_start: 0.9062 (tp30) cc_final: 0.8730 (tp30) REVERT: N 75 ASP cc_start: 0.9132 (t70) cc_final: 0.8761 (t0) outliers start: 41 outliers final: 15 residues processed: 373 average time/residue: 0.6917 time to fit residues: 270.8119 Evaluate side-chains 374 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 352 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 3 ARG Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain I residue 19 GLU Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 76 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 86 GLN B 84 GLN E 84 GLN K 14 ASN K 84 GLN L 84 GLN L 86 GLN M 84 GLN M 86 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.067041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.053497 restraints weight = 19775.835| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 3.12 r_work: 0.2432 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 9968 Z= 0.207 Angle : 0.521 5.600 13398 Z= 0.269 Chirality : 0.037 0.136 1568 Planarity : 0.003 0.031 1722 Dihedral : 3.407 12.477 1386 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.99 % Allowed : 23.48 % Favored : 71.53 % 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: 1.39 (0.25), residues: 1246 helix: 1.11 (0.18), residues: 924 sheet: None (None), residues: 0 loop : 0.69 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 74 TYR 0.010 0.001 TYR D 64 PHE 0.017 0.002 PHE B 59 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 9968) covalent geometry : angle 0.52053 (13398) hydrogen bonds : bond 0.03918 ( 608) hydrogen bonds : angle 4.05510 ( 1824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 356 time to evaluate : 0.246 Fit side-chains REVERT: B 1 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6717 (tpt) REVERT: B 18 GLU cc_start: 0.9056 (tp30) cc_final: 0.8690 (tp30) REVERT: B 48 ASP cc_start: 0.8395 (p0) cc_final: 0.7838 (p0) REVERT: B 51 ASP cc_start: 0.9033 (m-30) cc_final: 0.8713 (m-30) REVERT: B 75 ASP cc_start: 0.8996 (t70) cc_final: 0.8643 (t0) REVERT: C 18 GLU cc_start: 0.9020 (tp30) cc_final: 0.8743 (tp30) REVERT: C 75 ASP cc_start: 0.8694 (t0) cc_final: 0.8431 (t0) REVERT: C 81 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8324 (mtm) REVERT: D 19 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8702 (mt-10) REVERT: D 81 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8091 (mtm) REVERT: D 86 GLN cc_start: 0.8363 (mm110) cc_final: 0.8160 (mt0) REVERT: E 3 ARG cc_start: 0.8393 (pmm-80) cc_final: 0.8140 (pmm-80) REVERT: E 19 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8747 (mt-10) REVERT: E 75 ASP cc_start: 0.8876 (t70) cc_final: 0.8446 (t0) REVERT: F 62 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: F 75 ASP cc_start: 0.9111 (t0) cc_final: 0.8783 (t0) REVERT: F 80 GLU cc_start: 0.5244 (mm-30) cc_final: 0.4723 (mm-30) REVERT: G 1 MET cc_start: 0.7228 (tpp) cc_final: 0.6272 (tmm) REVERT: G 3 ARG cc_start: 0.8129 (ptt180) cc_final: 0.7650 (mmm-85) REVERT: G 48 ASP cc_start: 0.8486 (p0) cc_final: 0.7744 (p0) REVERT: G 51 ASP cc_start: 0.9103 (m-30) cc_final: 0.8541 (m-30) REVERT: G 75 ASP cc_start: 0.9006 (t0) cc_final: 0.8701 (t0) REVERT: H 18 GLU cc_start: 0.9186 (tp30) cc_final: 0.8812 (tp30) REVERT: H 81 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8358 (mtm) REVERT: I 18 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8192 (tm-30) REVERT: I 19 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8640 (pt0) REVERT: I 48 ASP cc_start: 0.8346 (p0) cc_final: 0.8072 (p0) REVERT: I 51 ASP cc_start: 0.9051 (m-30) cc_final: 0.8790 (m-30) REVERT: J 19 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8671 (pm20) REVERT: J 48 ASP cc_start: 0.8509 (p0) cc_final: 0.8044 (p0) REVERT: J 51 ASP cc_start: 0.9256 (m-30) cc_final: 0.8856 (m-30) REVERT: J 74 ARG cc_start: 0.9029 (mtm-85) cc_final: 0.8787 (mtp180) REVERT: J 75 ASP cc_start: 0.9183 (t70) cc_final: 0.8894 (t0) REVERT: J 86 GLN cc_start: 0.8678 (mt0) cc_final: 0.8397 (mt0) REVERT: K 62 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8444 (mt-10) REVERT: K 75 ASP cc_start: 0.9190 (t0) cc_final: 0.8963 (t70) REVERT: L 19 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: L 75 ASP cc_start: 0.9138 (t0) cc_final: 0.8880 (t0) REVERT: N 10 ASP cc_start: 0.8892 (m-30) cc_final: 0.8601 (m-30) REVERT: N 18 GLU cc_start: 0.9114 (tp30) cc_final: 0.8693 (tp30) REVERT: N 75 ASP cc_start: 0.9124 (t70) cc_final: 0.8766 (t0) REVERT: N 81 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8099 (mtm) outliers start: 51 outliers final: 22 residues processed: 367 average time/residue: 0.6531 time to fit residues: 251.9235 Evaluate side-chains 380 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 348 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain I residue 19 GLU Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 76 MET Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 19 GLU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain N residue 76 MET Chi-restraints excluded: chain N residue 81 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 86 GLN B 84 GLN D 84 GLN D 86 GLN E 84 GLN K 84 GLN L 84 GLN L 86 GLN M 84 GLN M 86 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.069070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.055622 restraints weight = 19686.322| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.11 r_work: 0.2487 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9968 Z= 0.119 Angle : 0.476 8.685 13398 Z= 0.246 Chirality : 0.035 0.136 1568 Planarity : 0.003 0.024 1722 Dihedral : 3.268 12.727 1386 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.33 % Allowed : 25.73 % Favored : 70.94 % 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: 1.51 (0.25), residues: 1246 helix: 1.22 (0.18), residues: 924 sheet: None (None), residues: 0 loop : 0.68 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 74 TYR 0.007 0.001 TYR D 64 PHE 0.008 0.001 PHE B 59 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9968) covalent geometry : angle 0.47621 (13398) hydrogen bonds : bond 0.03229 ( 608) hydrogen bonds : angle 3.95937 ( 1824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 372 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8407 (p0) cc_final: 0.8068 (p0) REVERT: A 51 ASP cc_start: 0.8989 (m-30) cc_final: 0.8660 (m-30) REVERT: B 18 GLU cc_start: 0.9016 (tp30) cc_final: 0.8669 (tp30) REVERT: B 48 ASP cc_start: 0.8311 (p0) cc_final: 0.7733 (p0) REVERT: B 51 ASP cc_start: 0.9031 (m-30) cc_final: 0.8692 (m-30) REVERT: B 75 ASP cc_start: 0.8985 (t70) cc_final: 0.8635 (t0) REVERT: C 18 GLU cc_start: 0.9018 (tp30) cc_final: 0.8722 (tp30) REVERT: C 75 ASP cc_start: 0.8674 (t0) cc_final: 0.8385 (t0) REVERT: C 81 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8310 (mtm) REVERT: D 19 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8761 (mt-10) REVERT: D 81 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8053 (mtm) REVERT: E 3 ARG cc_start: 0.8314 (pmm-80) cc_final: 0.8032 (pmm-80) REVERT: E 19 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8703 (mt-10) REVERT: E 75 ASP cc_start: 0.8897 (t70) cc_final: 0.8476 (t0) REVERT: F 75 ASP cc_start: 0.9125 (t0) cc_final: 0.8791 (t0) REVERT: F 80 GLU cc_start: 0.5266 (mm-30) cc_final: 0.4970 (mm-30) REVERT: G 1 MET cc_start: 0.7289 (tpp) cc_final: 0.6316 (tmm) REVERT: G 3 ARG cc_start: 0.8096 (ptt180) cc_final: 0.7579 (mmm-85) REVERT: G 62 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8354 (mt-10) REVERT: G 75 ASP cc_start: 0.9032 (t0) cc_final: 0.8749 (t0) REVERT: H 18 GLU cc_start: 0.9166 (tp30) cc_final: 0.8776 (tp30) REVERT: I 48 ASP cc_start: 0.8302 (p0) cc_final: 0.7978 (p0) REVERT: I 51 ASP cc_start: 0.9054 (m-30) cc_final: 0.8690 (m-30) REVERT: I 75 ASP cc_start: 0.9061 (t70) cc_final: 0.8835 (OUTLIER) REVERT: J 6 ASP cc_start: 0.8825 (m-30) cc_final: 0.8344 (m-30) REVERT: J 19 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8598 (pm20) REVERT: J 48 ASP cc_start: 0.8437 (p0) cc_final: 0.7993 (p0) REVERT: J 51 ASP cc_start: 0.9253 (m-30) cc_final: 0.8856 (m-30) REVERT: J 75 ASP cc_start: 0.9201 (t70) cc_final: 0.8891 (t0) REVERT: K 62 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8455 (mt-10) REVERT: K 75 ASP cc_start: 0.9205 (t0) cc_final: 0.8995 (t70) REVERT: L 19 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8497 (pm20) REVERT: L 26 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.8686 (mptm) REVERT: L 75 ASP cc_start: 0.9124 (t0) cc_final: 0.8921 (t0) REVERT: M 34 GLU cc_start: 0.8775 (mp0) cc_final: 0.8558 (mp0) REVERT: M 51 ASP cc_start: 0.9095 (m-30) cc_final: 0.8878 (m-30) REVERT: N 10 ASP cc_start: 0.8869 (m-30) cc_final: 0.8598 (m-30) REVERT: N 18 GLU cc_start: 0.9102 (tp30) cc_final: 0.8704 (tp30) REVERT: N 75 ASP cc_start: 0.9130 (t70) cc_final: 0.8790 (t0) outliers start: 34 outliers final: 12 residues processed: 378 average time/residue: 0.7116 time to fit residues: 282.7115 Evaluate side-chains 372 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 355 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain H residue 84 GLN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 19 GLU Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 29 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 84 GLN K 14 ASN K 79 GLN K 84 GLN L 84 GLN M 84 GLN M 86 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.068354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.055011 restraints weight = 19715.963| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 3.08 r_work: 0.2473 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9968 Z= 0.137 Angle : 0.499 8.051 13398 Z= 0.256 Chirality : 0.036 0.144 1568 Planarity : 0.003 0.024 1722 Dihedral : 3.265 12.204 1386 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.11 % Allowed : 27.01 % Favored : 68.88 % 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: 1.64 (0.25), residues: 1246 helix: 1.33 (0.18), residues: 924 sheet: None (None), residues: 0 loop : 0.64 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 74 TYR 0.008 0.001 TYR J 64 PHE 0.010 0.002 PHE B 59 HIS 0.001 0.000 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9968) covalent geometry : angle 0.49912 (13398) hydrogen bonds : bond 0.03378 ( 608) hydrogen bonds : angle 3.90175 ( 1824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 361 time to evaluate : 0.408 Fit side-chains REVERT: A 48 ASP cc_start: 0.8398 (p0) cc_final: 0.8034 (p0) REVERT: A 51 ASP cc_start: 0.8973 (m-30) cc_final: 0.8666 (m-30) REVERT: B 18 GLU cc_start: 0.9013 (tp30) cc_final: 0.8679 (tp30) REVERT: B 48 ASP cc_start: 0.8292 (p0) cc_final: 0.7721 (p0) REVERT: B 51 ASP cc_start: 0.9038 (m-30) cc_final: 0.8693 (m-30) REVERT: B 75 ASP cc_start: 0.9027 (t70) cc_final: 0.8692 (t0) REVERT: C 18 GLU cc_start: 0.9017 (tp30) cc_final: 0.8700 (tp30) REVERT: C 75 ASP cc_start: 0.8652 (t0) cc_final: 0.8332 (t0) REVERT: C 81 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8302 (mtm) REVERT: D 19 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8706 (mt-10) REVERT: D 81 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8077 (mtm) REVERT: E 3 ARG cc_start: 0.8291 (pmm-80) cc_final: 0.7996 (pmm-80) REVERT: E 75 ASP cc_start: 0.8886 (t70) cc_final: 0.8479 (t0) REVERT: F 75 ASP cc_start: 0.9143 (t0) cc_final: 0.8820 (t0) REVERT: F 80 GLU cc_start: 0.4967 (mm-30) cc_final: 0.4476 (mm-30) REVERT: G 1 MET cc_start: 0.7265 (tpp) cc_final: 0.6272 (tmm) REVERT: G 3 ARG cc_start: 0.8120 (ptt180) cc_final: 0.7585 (mmm-85) REVERT: G 48 ASP cc_start: 0.8507 (p0) cc_final: 0.7717 (p0) REVERT: G 51 ASP cc_start: 0.9108 (m-30) cc_final: 0.8555 (m-30) REVERT: G 62 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8353 (mt-10) REVERT: G 75 ASP cc_start: 0.9070 (t0) cc_final: 0.8801 (t0) REVERT: H 3 ARG cc_start: 0.8067 (pmt170) cc_final: 0.7533 (mmm-85) REVERT: H 18 GLU cc_start: 0.9158 (tp30) cc_final: 0.8780 (tp30) REVERT: H 26 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9052 (mptm) REVERT: I 18 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8163 (tm-30) REVERT: I 19 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8820 (mt-10) REVERT: I 48 ASP cc_start: 0.8287 (p0) cc_final: 0.8041 (p0) REVERT: I 51 ASP cc_start: 0.9018 (m-30) cc_final: 0.8765 (m-30) REVERT: I 75 ASP cc_start: 0.9070 (t70) cc_final: 0.8831 (t0) REVERT: J 6 ASP cc_start: 0.8818 (m-30) cc_final: 0.8345 (m-30) REVERT: J 19 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8625 (pm20) REVERT: J 48 ASP cc_start: 0.8424 (p0) cc_final: 0.7968 (p0) REVERT: J 51 ASP cc_start: 0.9247 (m-30) cc_final: 0.8826 (m-30) REVERT: J 75 ASP cc_start: 0.9216 (t70) cc_final: 0.8923 (t0) REVERT: K 51 ASP cc_start: 0.8990 (m-30) cc_final: 0.8775 (m-30) REVERT: K 62 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8404 (mt-10) REVERT: K 75 ASP cc_start: 0.9290 (t0) cc_final: 0.9059 (t70) REVERT: L 19 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8497 (pm20) REVERT: L 26 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.8691 (mptm) REVERT: L 75 ASP cc_start: 0.9097 (t0) cc_final: 0.8808 (t0) REVERT: M 51 ASP cc_start: 0.9090 (m-30) cc_final: 0.8874 (m-30) REVERT: N 6 ASP cc_start: 0.8916 (m-30) cc_final: 0.8624 (m-30) REVERT: N 10 ASP cc_start: 0.8861 (m-30) cc_final: 0.8581 (m-30) REVERT: N 18 GLU cc_start: 0.9113 (tp30) cc_final: 0.8682 (tp30) REVERT: N 75 ASP cc_start: 0.9133 (t70) cc_final: 0.8805 (t0) outliers start: 42 outliers final: 17 residues processed: 370 average time/residue: 0.6398 time to fit residues: 249.0039 Evaluate side-chains 378 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 354 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 84 GLN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 76 MET Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 19 GLU Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 29 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 86 GLN B 84 GLN D 84 GLN D 86 GLN I 84 GLN K 14 ASN K 84 GLN L 84 GLN L 86 GLN M 84 GLN M 86 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.065855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.052429 restraints weight = 19718.000| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 3.12 r_work: 0.2404 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 9968 Z= 0.263 Angle : 0.602 9.581 13398 Z= 0.303 Chirality : 0.040 0.155 1568 Planarity : 0.003 0.026 1722 Dihedral : 3.498 13.056 1386 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.21 % Allowed : 27.40 % Favored : 68.40 % 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: 1.64 (0.25), residues: 1246 helix: 1.34 (0.19), residues: 924 sheet: None (None), residues: 0 loop : 0.62 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 74 TYR 0.011 0.001 TYR D 64 PHE 0.019 0.002 PHE B 59 HIS 0.001 0.000 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 9968) covalent geometry : angle 0.60224 (13398) hydrogen bonds : bond 0.04302 ( 608) hydrogen bonds : angle 4.01006 ( 1824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 351 time to evaluate : 0.253 Fit side-chains REVERT: B 48 ASP cc_start: 0.8353 (p0) cc_final: 0.7856 (p0) REVERT: B 51 ASP cc_start: 0.9013 (m-30) cc_final: 0.8686 (m-30) REVERT: B 75 ASP cc_start: 0.9013 (t70) cc_final: 0.8690 (t0) REVERT: C 18 GLU cc_start: 0.9037 (tp30) cc_final: 0.8705 (tp30) REVERT: C 75 ASP cc_start: 0.8715 (t0) cc_final: 0.8450 (t0) REVERT: C 81 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8331 (mtm) REVERT: C 86 GLN cc_start: 0.8316 (mt0) cc_final: 0.8113 (mt0) REVERT: D 19 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8654 (mt-10) REVERT: D 62 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8361 (mt-10) REVERT: D 74 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8732 (ptp90) REVERT: D 81 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8133 (mtm) REVERT: E 3 ARG cc_start: 0.8277 (pmm-80) cc_final: 0.7969 (pmm-80) REVERT: E 75 ASP cc_start: 0.8872 (t70) cc_final: 0.8470 (t0) REVERT: F 75 ASP cc_start: 0.9164 (t0) cc_final: 0.8868 (t0) REVERT: F 80 GLU cc_start: 0.5268 (mm-30) cc_final: 0.4962 (mm-30) REVERT: G 1 MET cc_start: 0.7268 (tpp) cc_final: 0.6281 (tmm) REVERT: G 3 ARG cc_start: 0.8079 (ptt180) cc_final: 0.7630 (mmm-85) REVERT: G 48 ASP cc_start: 0.8487 (p0) cc_final: 0.7728 (p0) REVERT: G 51 ASP cc_start: 0.9117 (m-30) cc_final: 0.8557 (m-30) REVERT: G 75 ASP cc_start: 0.9094 (t0) cc_final: 0.8856 (t0) REVERT: H 3 ARG cc_start: 0.8111 (pmt170) cc_final: 0.7552 (mmm-85) REVERT: H 18 GLU cc_start: 0.9192 (tp30) cc_final: 0.8762 (tp30) REVERT: H 26 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9035 (mptm) REVERT: I 18 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8214 (tm-30) REVERT: I 51 ASP cc_start: 0.9091 (m-30) cc_final: 0.8785 (m-30) REVERT: I 75 ASP cc_start: 0.9064 (t70) cc_final: 0.8797 (t0) REVERT: J 48 ASP cc_start: 0.8499 (p0) cc_final: 0.8097 (p0) REVERT: J 51 ASP cc_start: 0.9235 (m-30) cc_final: 0.8842 (m-30) REVERT: J 75 ASP cc_start: 0.9193 (t70) cc_final: 0.8900 (t0) REVERT: K 62 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8528 (mt-10) REVERT: K 75 ASP cc_start: 0.9314 (t0) cc_final: 0.9086 (t0) REVERT: K 81 MET cc_start: 0.8944 (tpp) cc_final: 0.8687 (mmm) REVERT: L 19 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8500 (pm20) REVERT: L 26 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.8585 (mptm) REVERT: N 6 ASP cc_start: 0.8872 (m-30) cc_final: 0.8620 (m-30) REVERT: N 10 ASP cc_start: 0.8897 (m-30) cc_final: 0.8654 (m-30) REVERT: N 18 GLU cc_start: 0.9174 (tp30) cc_final: 0.8727 (tp30) REVERT: N 48 ASP cc_start: 0.8514 (p0) cc_final: 0.8310 (p0) REVERT: N 75 ASP cc_start: 0.9142 (t70) cc_final: 0.8795 (t0) REVERT: N 81 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8094 (mtm) outliers start: 43 outliers final: 18 residues processed: 363 average time/residue: 0.6396 time to fit residues: 243.8924 Evaluate side-chains 375 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 349 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 84 GLN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 19 GLU Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain N residue 81 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 58 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 86 GLN B 84 GLN D 84 GLN E 84 GLN K 14 ASN K 84 GLN L 84 GLN L 86 GLN M 84 GLN M 86 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.069433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.055847 restraints weight = 19525.280| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 3.16 r_work: 0.2484 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9968 Z= 0.116 Angle : 0.518 9.021 13398 Z= 0.267 Chirality : 0.035 0.135 1568 Planarity : 0.003 0.024 1722 Dihedral : 3.292 12.709 1386 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.13 % Allowed : 28.57 % Favored : 68.30 % 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: 1.67 (0.25), residues: 1246 helix: 1.36 (0.18), residues: 924 sheet: None (None), residues: 0 loop : 0.63 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 74 TYR 0.007 0.001 TYR J 64 PHE 0.008 0.001 PHE F 23 HIS 0.000 0.000 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9968) covalent geometry : angle 0.51797 (13398) hydrogen bonds : bond 0.03153 ( 608) hydrogen bonds : angle 3.92910 ( 1824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 373 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8257 (pt0) REVERT: A 48 ASP cc_start: 0.8435 (p0) cc_final: 0.7954 (p0) REVERT: A 51 ASP cc_start: 0.9021 (m-30) cc_final: 0.8727 (m-30) REVERT: B 18 GLU cc_start: 0.9018 (tp30) cc_final: 0.8668 (tp30) REVERT: B 48 ASP cc_start: 0.8222 (p0) cc_final: 0.7683 (p0) REVERT: B 51 ASP cc_start: 0.9009 (m-30) cc_final: 0.8675 (m-30) REVERT: B 75 ASP cc_start: 0.9010 (t70) cc_final: 0.8685 (t0) REVERT: C 18 GLU cc_start: 0.9032 (tp30) cc_final: 0.8714 (tp30) REVERT: C 75 ASP cc_start: 0.8665 (t0) cc_final: 0.8348 (t0) REVERT: C 81 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8304 (mtm) REVERT: C 86 GLN cc_start: 0.8327 (mt0) cc_final: 0.8008 (mt0) REVERT: D 19 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8724 (mt-10) REVERT: D 74 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8651 (ptp90) REVERT: E 3 ARG cc_start: 0.8271 (pmm-80) cc_final: 0.7943 (pmm-80) REVERT: E 75 ASP cc_start: 0.8877 (t70) cc_final: 0.8482 (t0) REVERT: F 75 ASP cc_start: 0.9139 (t0) cc_final: 0.8837 (t0) REVERT: F 80 GLU cc_start: 0.4946 (mm-30) cc_final: 0.4669 (mm-30) REVERT: G 1 MET cc_start: 0.7255 (tpp) cc_final: 0.6138 (tmm) REVERT: G 3 ARG cc_start: 0.8086 (ptt180) cc_final: 0.7548 (mmm-85) REVERT: G 75 ASP cc_start: 0.9086 (t0) cc_final: 0.8856 (t0) REVERT: H 18 GLU cc_start: 0.9167 (tp30) cc_final: 0.8721 (tp30) REVERT: H 26 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9015 (mptm) REVERT: I 18 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8111 (tm-30) REVERT: I 48 ASP cc_start: 0.8488 (p0) cc_final: 0.8141 (p0) REVERT: I 51 ASP cc_start: 0.9065 (m-30) cc_final: 0.8844 (m-30) REVERT: I 75 ASP cc_start: 0.9042 (t70) cc_final: 0.8769 (t0) REVERT: J 6 ASP cc_start: 0.8709 (m-30) cc_final: 0.8293 (m-30) REVERT: J 19 GLU cc_start: 0.8834 (pm20) cc_final: 0.8550 (pm20) REVERT: J 48 ASP cc_start: 0.8425 (p0) cc_final: 0.8010 (p0) REVERT: J 51 ASP cc_start: 0.9236 (m-30) cc_final: 0.8838 (m-30) REVERT: J 75 ASP cc_start: 0.9209 (t70) cc_final: 0.8906 (t0) REVERT: K 62 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8483 (mt-10) REVERT: K 75 ASP cc_start: 0.9302 (t0) cc_final: 0.9074 (t0) REVERT: L 19 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8491 (pm20) REVERT: L 26 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8729 (mptm) REVERT: L 33 ARG cc_start: 0.9064 (mtm-85) cc_final: 0.8687 (mtm-85) REVERT: L 34 GLU cc_start: 0.8780 (pm20) cc_final: 0.8566 (pm20) REVERT: M 34 GLU cc_start: 0.8756 (mp0) cc_final: 0.8522 (mp0) REVERT: N 6 ASP cc_start: 0.8884 (m-30) cc_final: 0.8598 (m-30) REVERT: N 10 ASP cc_start: 0.8861 (m-30) cc_final: 0.8606 (m-30) REVERT: N 18 GLU cc_start: 0.9141 (tp30) cc_final: 0.8651 (tp30) REVERT: N 62 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8428 (mt-10) REVERT: N 75 ASP cc_start: 0.9145 (t70) cc_final: 0.8819 (t0) outliers start: 32 outliers final: 14 residues processed: 380 average time/residue: 0.6226 time to fit residues: 248.5362 Evaluate side-chains 385 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 363 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 84 GLN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 19 GLU Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain N residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 86 GLN B 84 GLN D 84 GLN E 84 GLN F 71 ASN I 84 GLN K 14 ASN K 84 GLN L 84 GLN L 86 GLN M 84 GLN N 86 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.068417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.054585 restraints weight = 19449.186| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 3.19 r_work: 0.2462 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9968 Z= 0.140 Angle : 0.545 9.100 13398 Z= 0.277 Chirality : 0.036 0.153 1568 Planarity : 0.003 0.024 1722 Dihedral : 3.315 12.628 1386 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.35 % Allowed : 29.84 % Favored : 67.81 % 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: 1.66 (0.25), residues: 1246 helix: 1.36 (0.18), residues: 924 sheet: None (None), residues: 0 loop : 0.59 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 74 TYR 0.008 0.001 TYR D 64 PHE 0.010 0.002 PHE B 59 HIS 0.000 0.000 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9968) covalent geometry : angle 0.54485 (13398) hydrogen bonds : bond 0.03371 ( 608) hydrogen bonds : angle 3.91621 ( 1824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 363 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8347 (p0) cc_final: 0.7889 (p0) REVERT: A 51 ASP cc_start: 0.9002 (m-30) cc_final: 0.8721 (m-30) REVERT: B 18 GLU cc_start: 0.9055 (tp30) cc_final: 0.8706 (tp30) REVERT: B 48 ASP cc_start: 0.8192 (p0) cc_final: 0.7626 (p0) REVERT: B 51 ASP cc_start: 0.9016 (m-30) cc_final: 0.8672 (m-30) REVERT: B 75 ASP cc_start: 0.9039 (t70) cc_final: 0.8707 (t0) REVERT: C 18 GLU cc_start: 0.9029 (tp30) cc_final: 0.8703 (tp30) REVERT: C 75 ASP cc_start: 0.8659 (t0) cc_final: 0.8357 (t0) REVERT: C 81 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8334 (mtm) REVERT: C 86 GLN cc_start: 0.8302 (mt0) cc_final: 0.7914 (mt0) REVERT: D 19 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8702 (mt-10) REVERT: D 74 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8639 (ptp90) REVERT: E 3 ARG cc_start: 0.8246 (pmm-80) cc_final: 0.7914 (pmm-80) REVERT: E 75 ASP cc_start: 0.8876 (t70) cc_final: 0.8480 (t0) REVERT: F 75 ASP cc_start: 0.9148 (t0) cc_final: 0.8848 (t0) REVERT: F 80 GLU cc_start: 0.5011 (mm-30) cc_final: 0.4571 (mm-30) REVERT: G 1 MET cc_start: 0.7274 (tpp) cc_final: 0.6095 (tmm) REVERT: G 3 ARG cc_start: 0.8088 (ptt180) cc_final: 0.7576 (mmm-85) REVERT: G 75 ASP cc_start: 0.9100 (t0) cc_final: 0.8883 (t0) REVERT: H 18 GLU cc_start: 0.9180 (tp30) cc_final: 0.8735 (tp30) REVERT: I 18 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8115 (tm-30) REVERT: I 48 ASP cc_start: 0.8564 (p0) cc_final: 0.8199 (p0) REVERT: I 51 ASP cc_start: 0.9178 (m-30) cc_final: 0.8786 (m-30) REVERT: I 75 ASP cc_start: 0.9059 (t70) cc_final: 0.8788 (t0) REVERT: J 6 ASP cc_start: 0.8764 (m-30) cc_final: 0.8317 (m-30) REVERT: J 19 GLU cc_start: 0.8821 (pm20) cc_final: 0.8543 (pm20) REVERT: J 48 ASP cc_start: 0.8397 (p0) cc_final: 0.7963 (p0) REVERT: J 51 ASP cc_start: 0.9235 (m-30) cc_final: 0.8826 (m-30) REVERT: J 75 ASP cc_start: 0.9203 (t70) cc_final: 0.8903 (t0) REVERT: K 1 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6566 (mtt) REVERT: K 62 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8417 (mt-10) REVERT: K 75 ASP cc_start: 0.9340 (t0) cc_final: 0.9109 (t0) REVERT: L 19 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8461 (pm20) REVERT: L 26 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.8781 (mptm) REVERT: L 33 ARG cc_start: 0.9055 (mtm-85) cc_final: 0.8809 (mtm-85) REVERT: L 34 GLU cc_start: 0.8796 (pm20) cc_final: 0.8587 (pm20) REVERT: M 34 GLU cc_start: 0.8755 (mp0) cc_final: 0.8522 (mp0) REVERT: N 6 ASP cc_start: 0.8887 (m-30) cc_final: 0.8607 (m-30) REVERT: N 10 ASP cc_start: 0.8884 (m-30) cc_final: 0.8629 (m-30) REVERT: N 18 GLU cc_start: 0.9181 (tp30) cc_final: 0.8726 (tp30) REVERT: N 19 GLU cc_start: 0.8931 (pm20) cc_final: 0.8631 (pm20) REVERT: N 62 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8397 (mt-10) REVERT: N 75 ASP cc_start: 0.9150 (t70) cc_final: 0.8819 (t0) outliers start: 24 outliers final: 14 residues processed: 369 average time/residue: 0.6890 time to fit residues: 267.1339 Evaluate side-chains 379 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 358 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 84 GLN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 19 GLU Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain N residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN B 84 GLN E 84 GLN F 71 ASN I 84 GLN K 14 ASN K 84 GLN L 84 GLN L 86 GLN M 84 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.068579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.054864 restraints weight = 19649.392| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 3.18 r_work: 0.2460 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9968 Z= 0.141 Angle : 0.543 9.103 13398 Z= 0.277 Chirality : 0.036 0.142 1568 Planarity : 0.003 0.024 1722 Dihedral : 3.320 12.550 1386 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.05 % Allowed : 30.04 % Favored : 67.91 % 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: 1.68 (0.25), residues: 1246 helix: 1.38 (0.18), residues: 924 sheet: None (None), residues: 0 loop : 0.58 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 74 TYR 0.008 0.001 TYR D 64 PHE 0.009 0.002 PHE B 59 HIS 0.000 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9968) covalent geometry : angle 0.54307 (13398) hydrogen bonds : bond 0.03350 ( 608) hydrogen bonds : angle 3.87666 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4005.70 seconds wall clock time: 68 minutes 30.92 seconds (4110.92 seconds total)