Starting phenix.real_space_refine on Sat Aug 23 16:51:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbn_16546/08_2025/8cbn_16546.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbn_16546/08_2025/8cbn_16546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cbn_16546/08_2025/8cbn_16546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbn_16546/08_2025/8cbn_16546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cbn_16546/08_2025/8cbn_16546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbn_16546/08_2025/8cbn_16546.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 15 5.16 5 C 7698 2.51 5 N 2540 2.21 5 O 3116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13669 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3055 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3095 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "L" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 3.41, per 1000 atoms: 0.25 Number of scatterers: 13669 At special positions: 0 Unit cell: (81.144, 139.104, 129.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 300 15.00 O 3116 8.00 N 2540 7.00 C 7698 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: 1.06 Conformation dependent library (CDL) restraints added in 464.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 58.1% alpha, 5.1% beta 125 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.520A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.790A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.647A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.516A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.542A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.586A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.957A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.734A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 102 through 122 removed outlier: 3.543A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.765A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.943A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.516A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.515A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.542A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.586A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.956A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.734A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 102 through 122 removed outlier: 3.543A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 87 removed outlier: 5.137A pdb=" N ASP K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN K 86 " --> pdb=" O TRP K 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.690A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.555A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.570A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.621A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.684A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.629A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 87 removed outlier: 5.136A pdb=" N ASP L 85 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN L 86 " --> pdb=" O TRP L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.151A pdb=" N ARG B 45 " --> pdb=" O ILE A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.434A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.172A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.168A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.144A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 50 through 51 removed outlier: 3.622A pdb=" N PHE K 43 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA K 13 " --> pdb=" O TRP K 21 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA K 23 " --> pdb=" O ILE K 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE K 11 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 50 through 51 removed outlier: 3.623A pdb=" N PHE L 43 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA L 13 " --> pdb=" O TRP L 21 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA L 23 " --> pdb=" O ILE L 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE L 11 " --> pdb=" O ALA L 23 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2357 1.33 - 1.45: 4911 1.45 - 1.57: 6654 1.57 - 1.69: 598 1.69 - 1.81: 30 Bond restraints: 14550 Sorted by residual: bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.757 0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.763 0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.52e+00 bond pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" CB ARG F 78 " pdb=" CG ARG F 78 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 ... (remaining 14545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 19913 1.59 - 3.18: 951 3.18 - 4.78: 51 4.78 - 6.37: 13 6.37 - 7.96: 7 Bond angle restraints: 20935 Sorted by residual: angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 120.20 125.90 -5.70 1.50e+00 4.44e-01 1.45e+01 angle pdb=" C SER L 62 " pdb=" N GLU L 63 " pdb=" CA GLU L 63 " ideal model delta sigma weight residual 122.61 128.15 -5.54 1.56e+00 4.11e-01 1.26e+01 angle pdb=" C SER K 62 " pdb=" N GLU K 63 " pdb=" CA GLU K 63 " ideal model delta sigma weight residual 122.61 128.14 -5.53 1.56e+00 4.11e-01 1.26e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 120.20 125.02 -4.82 1.50e+00 4.44e-01 1.03e+01 angle pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " pdb=" P DC I 35 " ideal model delta sigma weight residual 120.20 124.97 -4.77 1.50e+00 4.44e-01 1.01e+01 ... (remaining 20930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 6580 34.29 - 68.57: 1388 68.57 - 102.86: 15 102.86 - 137.15: 2 137.15 - 171.44: 1 Dihedral angle restraints: 7986 sinusoidal: 5267 harmonic: 2719 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 48.56 171.44 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU K 53 " pdb=" C LEU K 53 " pdb=" N GLY K 54 " pdb=" CA GLY K 54 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1293 0.035 - 0.070: 832 0.070 - 0.105: 172 0.105 - 0.140: 40 0.140 - 0.175: 10 Chirality restraints: 2347 Sorted by residual: chirality pdb=" P DC I 21 " pdb=" OP1 DC I 21 " pdb=" OP2 DC I 21 " pdb=" O5' DC I 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.52 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB VAL L 90 " pdb=" CA VAL L 90 " pdb=" CG1 VAL L 90 " pdb=" CG2 VAL L 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 2344 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO E 66 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO G 80 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO C 80 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.037 5.00e-02 4.00e+02 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.68: 2 1.68 - 2.49: 54 2.49 - 3.29: 12951 3.29 - 4.10: 39079 4.10 - 4.90: 66074 Warning: very small nonbonded interaction distances. Nonbonded interactions: 118160 Sorted by model distance: nonbonded pdb=" OP1 DA I -69 " pdb=" NZ LYS L 73 " model vdw 0.876 3.120 nonbonded pdb=" OP1 DA I -69 " pdb=" CE LYS L 73 " model vdw 0.936 3.440 nonbonded pdb=" OP1 DG I -68 " pdb=" CD PRO L 19 " model vdw 1.751 3.440 nonbonded pdb=" O3' DA I -69 " pdb=" NH2 ARG L 74 " model vdw 1.840 3.120 nonbonded pdb=" P DA I -69 " pdb=" CE LYS L 73 " model vdw 1.967 3.800 ... (remaining 118155 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.690 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.230 Find NCS groups from input model: 0.120 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.008 0.077 14550 Z= 0.361 Angle : 0.720 7.960 20935 Z= 0.424 Chirality : 0.044 0.175 2347 Planarity : 0.007 0.069 1614 Dihedral : 25.785 171.435 6230 Min Nonbonded Distance : 0.876 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.28 % Allowed : 8.75 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.72 (0.17), residues: 913 helix: -4.46 (0.09), residues: 538 sheet: -4.09 (0.69), residues: 34 loop : -2.16 (0.26), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 55 TYR 0.012 0.002 TYR B 72 PHE 0.013 0.002 PHE K 45 TRP 0.005 0.002 TRP L 82 HIS 0.004 0.001 HIS L 20 Details of bonding type rmsd covalent geometry : bond 0.00816 (14550) covalent geometry : angle 0.72022 (20935) hydrogen bonds : bond 0.31427 ( 667) hydrogen bonds : angle 10.67049 ( 1658) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 310 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.8817 (mttt) cc_final: 0.8467 (mttp) REVERT: B 98 TYR cc_start: 0.8973 (m-10) cc_final: 0.8159 (m-10) REVERT: C 34 LEU cc_start: 0.8953 (mt) cc_final: 0.8726 (mm) REVERT: C 110 ASN cc_start: 0.8654 (t0) cc_final: 0.8437 (t0) REVERT: C 115 LEU cc_start: 0.8384 (mt) cc_final: 0.7998 (mp) REVERT: D 59 MET cc_start: 0.8367 (mmm) cc_final: 0.8047 (mmm) REVERT: D 91 ILE cc_start: 0.8561 (mm) cc_final: 0.8306 (mt) REVERT: D 103 LEU cc_start: 0.8637 (mt) cc_final: 0.8277 (mt) REVERT: F 43 VAL cc_start: 0.9461 (t) cc_final: 0.9260 (t) REVERT: F 73 THR cc_start: 0.7936 (m) cc_final: 0.7699 (m) REVERT: H 87 THR cc_start: 0.8808 (p) cc_final: 0.8441 (t) REVERT: A 90 MET cc_start: 0.8080 (mmm) cc_final: 0.7870 (mmt) REVERT: A 120 MET cc_start: 0.7883 (mtp) cc_final: 0.7414 (mtt) REVERT: A 126 LEU cc_start: 0.9415 (tp) cc_final: 0.9168 (tp) REVERT: E 41 TYR cc_start: 0.8515 (m-80) cc_final: 0.8265 (m-10) REVERT: E 60 LEU cc_start: 0.8938 (mt) cc_final: 0.8699 (mt) REVERT: E 119 ILE cc_start: 0.9261 (pt) cc_final: 0.9011 (pt) REVERT: E 125 GLN cc_start: 0.8627 (mt0) cc_final: 0.8360 (mt0) outliers start: 18 outliers final: 7 residues processed: 323 average time/residue: 0.1559 time to fit residues: 64.6275 Evaluate side-chains 240 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 233 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 73 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 68 ASN C 73 ASN D 44 GLN D 92 GLN F 18 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 92 GLN K 64 ASN K 86 ASN A 108 ASN A 113 HIS L 64 ASN L 86 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.168513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105827 restraints weight = 20770.790| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.53 r_work: 0.3028 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14550 Z= 0.172 Angle : 0.621 8.844 20935 Z= 0.367 Chirality : 0.037 0.176 2347 Planarity : 0.006 0.056 1614 Dihedral : 29.595 156.663 4342 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.65 % Allowed : 17.49 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.24), residues: 913 helix: -1.60 (0.19), residues: 545 sheet: -4.32 (0.90), residues: 20 loop : -1.36 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 129 TYR 0.011 0.002 TYR G 57 PHE 0.012 0.001 PHE A 67 TRP 0.003 0.001 TRP K 82 HIS 0.008 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00375 (14550) covalent geometry : angle 0.62082 (20935) hydrogen bonds : bond 0.06471 ( 667) hydrogen bonds : angle 3.30816 ( 1658) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 256 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9233 (mttt) cc_final: 0.8801 (mttp) REVERT: B 93 GLN cc_start: 0.9017 (mt0) cc_final: 0.8772 (mt0) REVERT: B 98 TYR cc_start: 0.9018 (m-10) cc_final: 0.8395 (m-10) REVERT: C 34 LEU cc_start: 0.8951 (mt) cc_final: 0.8431 (mt) REVERT: C 73 ASN cc_start: 0.7587 (t0) cc_final: 0.6903 (t0) REVERT: C 115 LEU cc_start: 0.8570 (mt) cc_final: 0.8217 (mp) REVERT: D 59 MET cc_start: 0.8781 (mmm) cc_final: 0.8358 (tpp) REVERT: D 68 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: F 73 THR cc_start: 0.8796 (m) cc_final: 0.8500 (m) REVERT: F 74 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: F 84 MET cc_start: 0.8569 (mmm) cc_final: 0.8338 (mmt) REVERT: G 92 GLU cc_start: 0.8477 (pm20) cc_final: 0.8136 (pm20) REVERT: G 110 ASN cc_start: 0.8834 (t0) cc_final: 0.8531 (t0) REVERT: H 51 ILE cc_start: 0.9058 (tt) cc_final: 0.8858 (tt) REVERT: H 68 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8434 (mm-30) REVERT: H 109 SER cc_start: 0.9031 (t) cc_final: 0.8813 (p) REVERT: H 117 LYS cc_start: 0.8497 (tppp) cc_final: 0.7696 (ttpp) REVERT: K 15 MET cc_start: 0.6636 (mtt) cc_final: 0.6266 (mtt) REVERT: K 70 LYS cc_start: 0.4038 (mmtm) cc_final: 0.3824 (mmtm) REVERT: A 41 TYR cc_start: 0.8113 (m-80) cc_final: 0.7880 (m-80) REVERT: A 65 LEU cc_start: 0.8588 (mm) cc_final: 0.8326 (mt) REVERT: A 79 LYS cc_start: 0.9009 (tttm) cc_final: 0.8484 (tttp) REVERT: A 90 MET cc_start: 0.8525 (mmm) cc_final: 0.8133 (mmt) REVERT: A 118 THR cc_start: 0.9534 (m) cc_final: 0.9270 (p) REVERT: A 120 MET cc_start: 0.7666 (mtp) cc_final: 0.7436 (mtp) REVERT: E 39 HIS cc_start: 0.8730 (t70) cc_final: 0.8298 (t70) REVERT: E 76 GLN cc_start: 0.9252 (tp40) cc_final: 0.8988 (mm-40) REVERT: E 105 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8896 (mm-30) outliers start: 13 outliers final: 7 residues processed: 265 average time/residue: 0.1348 time to fit residues: 48.2844 Evaluate side-chains 246 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 236 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 118 optimal weight: 30.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS A 39 HIS E 93 GLN E 108 ASN L 78 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.158036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.093356 restraints weight = 20876.276| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.53 r_work: 0.2845 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14550 Z= 0.215 Angle : 0.621 8.375 20935 Z= 0.360 Chirality : 0.037 0.130 2347 Planarity : 0.005 0.049 1614 Dihedral : 29.590 148.697 4329 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.17 % Allowed : 21.29 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.26), residues: 913 helix: 0.01 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -1.54 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 83 TYR 0.030 0.002 TYR H 80 PHE 0.012 0.001 PHE E 67 TRP 0.003 0.001 TRP L 21 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00489 (14550) covalent geometry : angle 0.62105 (20935) hydrogen bonds : bond 0.06569 ( 667) hydrogen bonds : angle 3.10045 ( 1658) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 275 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9621 (mttt) cc_final: 0.9247 (mttp) REVERT: B 84 MET cc_start: 0.8153 (mmt) cc_final: 0.7763 (mmt) REVERT: B 88 TYR cc_start: 0.9001 (m-10) cc_final: 0.8693 (m-10) REVERT: B 98 TYR cc_start: 0.9243 (m-10) cc_final: 0.8575 (m-10) REVERT: C 73 ASN cc_start: 0.8015 (t0) cc_final: 0.7308 (t0) REVERT: C 94 ASN cc_start: 0.8621 (t0) cc_final: 0.8107 (t0) REVERT: D 82 LYS cc_start: 0.9217 (ttmm) cc_final: 0.8999 (mmmm) REVERT: D 122 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6813 (ttpp) REVERT: F 63 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8585 (mt-10) REVERT: F 73 THR cc_start: 0.9259 (m) cc_final: 0.8994 (m) REVERT: F 78 ARG cc_start: 0.9250 (mtt90) cc_final: 0.8660 (mtp180) REVERT: G 33 LEU cc_start: 0.8987 (mt) cc_final: 0.8783 (mt) REVERT: G 35 ARG cc_start: 0.8948 (ttm110) cc_final: 0.8659 (ttm110) REVERT: G 39 TYR cc_start: 0.9230 (m-80) cc_final: 0.8596 (m-80) REVERT: G 77 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7909 (ttm-80) REVERT: G 90 ASP cc_start: 0.9051 (t70) cc_final: 0.8001 (t0) REVERT: G 92 GLU cc_start: 0.8599 (pm20) cc_final: 0.8355 (pm20) REVERT: H 109 SER cc_start: 0.9104 (t) cc_final: 0.8880 (p) REVERT: H 117 LYS cc_start: 0.8623 (tppp) cc_final: 0.8026 (ttpp) REVERT: K 14 LYS cc_start: 0.6971 (tppt) cc_final: 0.5756 (pttt) REVERT: K 16 LYS cc_start: 0.8407 (tppt) cc_final: 0.8171 (tppt) REVERT: K 70 LYS cc_start: 0.4175 (mmtm) cc_final: 0.3915 (mmtm) REVERT: A 41 TYR cc_start: 0.8969 (m-80) cc_final: 0.8595 (m-80) REVERT: A 42 ARG cc_start: 0.7282 (mmm-85) cc_final: 0.6597 (mmm-85) REVERT: A 57 SER cc_start: 0.8921 (p) cc_final: 0.8370 (t) REVERT: A 59 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7790 (mp0) REVERT: A 79 LYS cc_start: 0.9198 (tttm) cc_final: 0.8945 (tttm) REVERT: A 85 GLN cc_start: 0.8747 (mt0) cc_final: 0.8361 (mt0) REVERT: A 90 MET cc_start: 0.8809 (mmm) cc_final: 0.8582 (mmp) REVERT: A 120 MET cc_start: 0.8299 (mtp) cc_final: 0.8021 (mtp) REVERT: E 59 GLU cc_start: 0.8669 (mp0) cc_final: 0.8040 (mp0) REVERT: E 76 GLN cc_start: 0.9280 (tp40) cc_final: 0.8996 (mm-40) REVERT: E 108 ASN cc_start: 0.9367 (t0) cc_final: 0.9123 (t0) outliers start: 25 outliers final: 14 residues processed: 286 average time/residue: 0.1248 time to fit residues: 47.7486 Evaluate side-chains 267 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 251 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 85 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 112 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 73 ASN K 78 ASN A 39 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.155978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.089508 restraints weight = 21017.769| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.73 r_work: 0.2791 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14550 Z= 0.200 Angle : 0.595 7.893 20935 Z= 0.348 Chirality : 0.037 0.139 2347 Planarity : 0.004 0.046 1614 Dihedral : 29.426 150.576 4327 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.82 % Allowed : 23.83 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.27), residues: 913 helix: 0.75 (0.22), residues: 547 sheet: -4.22 (0.89), residues: 20 loop : -1.17 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 40 TYR 0.036 0.002 TYR D 80 PHE 0.010 0.001 PHE F 100 TRP 0.003 0.001 TRP K 82 HIS 0.009 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00454 (14550) covalent geometry : angle 0.59494 (20935) hydrogen bonds : bond 0.05865 ( 667) hydrogen bonds : angle 2.93082 ( 1658) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9538 (mttt) cc_final: 0.9243 (mttp) REVERT: B 98 TYR cc_start: 0.9106 (m-10) cc_final: 0.8535 (m-10) REVERT: C 73 ASN cc_start: 0.8219 (t0) cc_final: 0.7447 (t0) REVERT: C 100 VAL cc_start: 0.9782 (OUTLIER) cc_final: 0.9385 (p) REVERT: D 91 ILE cc_start: 0.8872 (mm) cc_final: 0.8508 (mt) REVERT: D 102 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: D 105 LYS cc_start: 0.9056 (tppp) cc_final: 0.8710 (mtmm) REVERT: D 122 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6975 (ttpp) REVERT: F 39 ARG cc_start: 0.8576 (mmt90) cc_final: 0.8273 (tpp-160) REVERT: F 78 ARG cc_start: 0.9203 (mtt90) cc_final: 0.8998 (mtm-85) REVERT: G 35 ARG cc_start: 0.8899 (ttm110) cc_final: 0.8648 (ttm110) REVERT: G 39 TYR cc_start: 0.9228 (m-80) cc_final: 0.8915 (m-80) REVERT: G 75 LYS cc_start: 0.8536 (mmtp) cc_final: 0.8236 (mmtm) REVERT: G 90 ASP cc_start: 0.8582 (t70) cc_final: 0.7322 (t70) REVERT: G 92 GLU cc_start: 0.8637 (pm20) cc_final: 0.8096 (pm20) REVERT: H 68 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8585 (mm-30) REVERT: H 80 TYR cc_start: 0.8689 (m-80) cc_final: 0.8273 (m-80) REVERT: H 90 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8588 (mp0) REVERT: H 102 GLU cc_start: 0.7891 (tp30) cc_final: 0.7547 (tp30) REVERT: H 105 LYS cc_start: 0.9304 (mmmm) cc_final: 0.9089 (mmmm) REVERT: H 117 LYS cc_start: 0.8421 (tppp) cc_final: 0.7829 (ttpp) REVERT: K 14 LYS cc_start: 0.6638 (tppt) cc_final: 0.4698 (mptt) REVERT: K 16 LYS cc_start: 0.8354 (tppt) cc_final: 0.7833 (tptp) REVERT: K 70 LYS cc_start: 0.4144 (mmtm) cc_final: 0.3880 (mmtm) REVERT: A 42 ARG cc_start: 0.7006 (mmm-85) cc_final: 0.6297 (mmm-85) REVERT: A 79 LYS cc_start: 0.9059 (tttm) cc_final: 0.8853 (tttm) REVERT: A 85 GLN cc_start: 0.8657 (mt0) cc_final: 0.8227 (mt0) REVERT: A 90 MET cc_start: 0.8329 (mmm) cc_final: 0.7909 (mmp) REVERT: A 120 MET cc_start: 0.8106 (mtp) cc_final: 0.7829 (mtp) REVERT: E 76 GLN cc_start: 0.9221 (tp40) cc_final: 0.8943 (mm-40) REVERT: E 105 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8908 (mm-30) REVERT: E 108 ASN cc_start: 0.9031 (t0) cc_final: 0.8801 (t0) outliers start: 38 outliers final: 25 residues processed: 278 average time/residue: 0.1263 time to fit residues: 47.2521 Evaluate side-chains 282 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.0060 chunk 111 optimal weight: 0.0770 chunk 96 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 73 ASN E 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.159376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.093464 restraints weight = 21133.838| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.79 r_work: 0.2854 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14550 Z= 0.143 Angle : 0.548 7.212 20935 Z= 0.322 Chirality : 0.034 0.152 2347 Planarity : 0.004 0.045 1614 Dihedral : 29.101 148.046 4327 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.55 % Allowed : 26.24 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.28), residues: 913 helix: 1.34 (0.23), residues: 550 sheet: -4.15 (0.90), residues: 20 loop : -1.01 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.045 0.001 TYR D 80 PHE 0.009 0.001 PHE E 67 TRP 0.003 0.000 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00309 (14550) covalent geometry : angle 0.54781 (20935) hydrogen bonds : bond 0.04937 ( 667) hydrogen bonds : angle 2.66004 ( 1658) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8714 (mm-30) REVERT: B 77 LYS cc_start: 0.9499 (mttt) cc_final: 0.9165 (mttm) REVERT: C 73 ASN cc_start: 0.7902 (t0) cc_final: 0.7202 (t0) REVERT: C 77 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7792 (tpp80) REVERT: C 94 ASN cc_start: 0.8165 (t0) cc_final: 0.7644 (t0) REVERT: D 39 TYR cc_start: 0.7783 (t80) cc_final: 0.7345 (t80) REVERT: D 49 THR cc_start: 0.8991 (m) cc_final: 0.8701 (p) REVERT: D 102 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7450 (mm-30) REVERT: D 105 LYS cc_start: 0.8969 (tppp) cc_final: 0.8593 (mtmm) REVERT: F 63 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8378 (mt-10) REVERT: F 84 MET cc_start: 0.7974 (mmm) cc_final: 0.7338 (mmm) REVERT: G 39 TYR cc_start: 0.9186 (m-80) cc_final: 0.8854 (m-80) REVERT: G 84 GLN cc_start: 0.9209 (tp40) cc_final: 0.8872 (tp40) REVERT: G 90 ASP cc_start: 0.8592 (t70) cc_final: 0.7642 (t0) REVERT: G 92 GLU cc_start: 0.8697 (pm20) cc_final: 0.8351 (pm20) REVERT: G 112 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7762 (mm110) REVERT: H 68 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8591 (mm-30) REVERT: H 80 TYR cc_start: 0.8582 (m-80) cc_final: 0.8188 (m-80) REVERT: H 90 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8608 (mp0) REVERT: H 102 GLU cc_start: 0.7813 (tp30) cc_final: 0.7522 (tp30) REVERT: H 117 LYS cc_start: 0.8424 (tppp) cc_final: 0.7864 (ttpp) REVERT: K 14 LYS cc_start: 0.6819 (tppt) cc_final: 0.4803 (mptt) REVERT: K 16 LYS cc_start: 0.8457 (tppt) cc_final: 0.7985 (tptm) REVERT: K 70 LYS cc_start: 0.3954 (mmtm) cc_final: 0.3734 (mmtm) REVERT: A 73 GLU cc_start: 0.9196 (tp30) cc_final: 0.8106 (tp30) REVERT: A 79 LYS cc_start: 0.9005 (tttm) cc_final: 0.8686 (tttp) REVERT: A 90 MET cc_start: 0.8239 (mmm) cc_final: 0.7963 (mmt) REVERT: A 108 ASN cc_start: 0.8901 (t0) cc_final: 0.8400 (t0) REVERT: A 120 MET cc_start: 0.7966 (mtp) cc_final: 0.7699 (mtt) REVERT: E 76 GLN cc_start: 0.9201 (tp40) cc_final: 0.8893 (mm-40) REVERT: E 90 MET cc_start: 0.8694 (tpp) cc_final: 0.8439 (mmm) outliers start: 28 outliers final: 17 residues processed: 273 average time/residue: 0.1336 time to fit residues: 48.9476 Evaluate side-chains 270 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 251 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 40.0000 chunk 22 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.157226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.091520 restraints weight = 21822.650| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.76 r_work: 0.2855 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14550 Z= 0.171 Angle : 0.565 7.052 20935 Z= 0.330 Chirality : 0.035 0.141 2347 Planarity : 0.004 0.043 1614 Dihedral : 29.207 146.851 4323 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.93 % Allowed : 25.98 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.28), residues: 913 helix: 1.47 (0.22), residues: 555 sheet: -4.13 (0.92), residues: 20 loop : -0.92 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.047 0.002 TYR D 80 PHE 0.011 0.001 PHE E 67 TRP 0.002 0.000 TRP K 82 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00384 (14550) covalent geometry : angle 0.56479 (20935) hydrogen bonds : bond 0.05502 ( 667) hydrogen bonds : angle 2.80189 ( 1658) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 260 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9539 (mttt) cc_final: 0.9234 (mttm) REVERT: B 98 TYR cc_start: 0.9193 (m-10) cc_final: 0.8644 (m-10) REVERT: C 73 ASN cc_start: 0.8545 (t0) cc_final: 0.7962 (t0) REVERT: C 77 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7999 (tpp80) REVERT: C 100 VAL cc_start: 0.9538 (t) cc_final: 0.9045 (p) REVERT: D 102 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7482 (mm-30) REVERT: D 105 LYS cc_start: 0.9086 (tppp) cc_final: 0.8707 (mtmm) REVERT: F 68 ASP cc_start: 0.9302 (m-30) cc_final: 0.9081 (m-30) REVERT: G 39 TYR cc_start: 0.9278 (m-80) cc_final: 0.8687 (m-80) REVERT: G 90 ASP cc_start: 0.8796 (t70) cc_final: 0.7663 (t70) REVERT: G 92 GLU cc_start: 0.8792 (pm20) cc_final: 0.8327 (pm20) REVERT: H 68 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8722 (mm-30) REVERT: H 80 TYR cc_start: 0.8809 (m-80) cc_final: 0.8355 (m-80) REVERT: H 84 SER cc_start: 0.8953 (m) cc_final: 0.8391 (p) REVERT: H 90 GLU cc_start: 0.8954 (mp0) cc_final: 0.8634 (mp0) REVERT: H 102 GLU cc_start: 0.7987 (tp30) cc_final: 0.7710 (tp30) REVERT: H 117 LYS cc_start: 0.8662 (tppp) cc_final: 0.8087 (ttpp) REVERT: K 16 LYS cc_start: 0.8512 (tppt) cc_final: 0.8012 (tptp) REVERT: K 70 LYS cc_start: 0.3959 (mmtm) cc_final: 0.3738 (mmtm) REVERT: A 90 MET cc_start: 0.8276 (mmm) cc_final: 0.7966 (mmt) REVERT: A 120 MET cc_start: 0.8247 (mtp) cc_final: 0.7996 (mtp) REVERT: E 105 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8824 (mm-30) outliers start: 31 outliers final: 24 residues processed: 272 average time/residue: 0.1227 time to fit residues: 45.5891 Evaluate side-chains 280 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN A 108 ASN E 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.154533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.088857 restraints weight = 21840.570| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.73 r_work: 0.2813 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14550 Z= 0.208 Angle : 0.604 6.924 20935 Z= 0.351 Chirality : 0.037 0.169 2347 Planarity : 0.004 0.047 1614 Dihedral : 29.242 145.976 4323 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.32 % Allowed : 25.60 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.28), residues: 913 helix: 1.51 (0.22), residues: 552 sheet: -3.91 (0.98), residues: 20 loop : -0.99 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 35 TYR 0.049 0.002 TYR D 80 PHE 0.010 0.001 PHE E 67 TRP 0.002 0.000 TRP K 21 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00476 (14550) covalent geometry : angle 0.60436 (20935) hydrogen bonds : bond 0.06062 ( 667) hydrogen bonds : angle 2.98208 ( 1658) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8873 (mm110) cc_final: 0.8619 (mm110) REVERT: B 77 LYS cc_start: 0.9602 (mttt) cc_final: 0.9363 (mttm) REVERT: B 92 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.8714 (ttt-90) REVERT: B 98 TYR cc_start: 0.9163 (m-10) cc_final: 0.8647 (m-10) REVERT: C 15 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7801 (ptpp) REVERT: C 73 ASN cc_start: 0.8730 (t0) cc_final: 0.8104 (t0) REVERT: C 75 LYS cc_start: 0.9169 (mmtp) cc_final: 0.8828 (mmmm) REVERT: C 77 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8087 (tpp80) REVERT: C 100 VAL cc_start: 0.9441 (t) cc_final: 0.8826 (p) REVERT: D 48 ASP cc_start: 0.8912 (m-30) cc_final: 0.8512 (p0) REVERT: D 91 ILE cc_start: 0.8989 (mm) cc_final: 0.8702 (mt) REVERT: D 102 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: D 105 LYS cc_start: 0.9149 (tppp) cc_final: 0.8719 (mtmm) REVERT: F 84 MET cc_start: 0.7951 (mmm) cc_final: 0.7415 (mmm) REVERT: F 92 ARG cc_start: 0.9027 (ttp80) cc_final: 0.8804 (ttp80) REVERT: G 39 TYR cc_start: 0.9284 (m-80) cc_final: 0.8783 (m-80) REVERT: G 90 ASP cc_start: 0.8610 (t70) cc_final: 0.7717 (t0) REVERT: G 92 GLU cc_start: 0.8845 (pm20) cc_final: 0.8461 (pm20) REVERT: H 68 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8723 (mm-30) REVERT: H 77 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8510 (mp) REVERT: H 80 TYR cc_start: 0.8808 (m-80) cc_final: 0.8162 (m-80) REVERT: H 84 SER cc_start: 0.9055 (m) cc_final: 0.8515 (p) REVERT: K 16 LYS cc_start: 0.8638 (tppt) cc_final: 0.8120 (tptp) REVERT: K 70 LYS cc_start: 0.4590 (mmtm) cc_final: 0.4357 (mmtm) REVERT: A 82 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8450 (mm) REVERT: A 85 GLN cc_start: 0.8682 (mt0) cc_final: 0.8281 (mt0) REVERT: A 90 MET cc_start: 0.8311 (mmm) cc_final: 0.8045 (mmt) REVERT: A 120 MET cc_start: 0.8473 (mtp) cc_final: 0.7893 (mtp) REVERT: A 123 ASP cc_start: 0.9153 (m-30) cc_final: 0.8821 (m-30) REVERT: E 54 TYR cc_start: 0.8919 (m-80) cc_final: 0.8526 (m-80) REVERT: E 105 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8895 (mm-30) REVERT: E 124 ILE cc_start: 0.9093 (mm) cc_final: 0.8860 (mm) outliers start: 42 outliers final: 33 residues processed: 284 average time/residue: 0.1280 time to fit residues: 49.0139 Evaluate side-chains 300 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 40.0000 chunk 26 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN E 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.154917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.089519 restraints weight = 21671.632| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.71 r_work: 0.2838 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14550 Z= 0.199 Angle : 0.595 7.689 20935 Z= 0.345 Chirality : 0.036 0.149 2347 Planarity : 0.004 0.043 1614 Dihedral : 29.164 145.346 4323 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.94 % Allowed : 26.62 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.28), residues: 913 helix: 1.64 (0.22), residues: 553 sheet: -3.71 (1.00), residues: 20 loop : -0.96 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 35 TYR 0.048 0.002 TYR D 80 PHE 0.010 0.001 PHE E 67 TRP 0.001 0.000 TRP K 82 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00454 (14550) covalent geometry : angle 0.59545 (20935) hydrogen bonds : bond 0.05782 ( 667) hydrogen bonds : angle 2.89461 ( 1658) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8861 (mm110) cc_final: 0.8610 (mm110) REVERT: B 77 LYS cc_start: 0.9586 (mttt) cc_final: 0.9342 (mttm) REVERT: B 98 TYR cc_start: 0.9158 (m-10) cc_final: 0.8655 (m-10) REVERT: C 15 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7413 (mtmm) REVERT: C 73 ASN cc_start: 0.8655 (t0) cc_final: 0.7953 (t0) REVERT: C 75 LYS cc_start: 0.9131 (mmtp) cc_final: 0.8782 (mmmm) REVERT: C 77 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7974 (tpp80) REVERT: C 100 VAL cc_start: 0.9490 (t) cc_final: 0.8944 (p) REVERT: D 48 ASP cc_start: 0.8895 (m-30) cc_final: 0.8492 (p0) REVERT: D 91 ILE cc_start: 0.8980 (mm) cc_final: 0.8686 (mt) REVERT: F 84 MET cc_start: 0.8061 (mmm) cc_final: 0.7616 (mmm) REVERT: G 39 TYR cc_start: 0.9267 (m-80) cc_final: 0.8854 (m-80) REVERT: G 90 ASP cc_start: 0.8609 (t70) cc_final: 0.7475 (t70) REVERT: G 92 GLU cc_start: 0.8841 (pm20) cc_final: 0.8352 (pm20) REVERT: H 68 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8719 (mm-30) REVERT: H 84 SER cc_start: 0.9073 (m) cc_final: 0.8530 (p) REVERT: K 16 LYS cc_start: 0.8653 (tppt) cc_final: 0.8209 (tptm) REVERT: K 70 LYS cc_start: 0.4642 (mmtm) cc_final: 0.4367 (mmtm) REVERT: A 42 ARG cc_start: 0.7602 (mmm-85) cc_final: 0.7310 (mmm-85) REVERT: A 79 LYS cc_start: 0.9138 (tttm) cc_final: 0.8726 (tttp) REVERT: A 82 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8361 (mm) REVERT: A 85 GLN cc_start: 0.8745 (mt0) cc_final: 0.8500 (mt0) REVERT: A 90 MET cc_start: 0.8267 (mmm) cc_final: 0.7983 (mmt) REVERT: A 120 MET cc_start: 0.8497 (mtp) cc_final: 0.7895 (mtp) REVERT: A 123 ASP cc_start: 0.9181 (m-30) cc_final: 0.8850 (m-30) REVERT: E 54 TYR cc_start: 0.8927 (m-80) cc_final: 0.8490 (m-80) REVERT: E 105 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8896 (mm-30) outliers start: 39 outliers final: 32 residues processed: 277 average time/residue: 0.1189 time to fit residues: 44.7953 Evaluate side-chains 294 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN E 39 HIS E 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.152626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.086831 restraints weight = 21892.974| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.71 r_work: 0.2810 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14550 Z= 0.248 Angle : 0.636 8.339 20935 Z= 0.365 Chirality : 0.039 0.144 2347 Planarity : 0.004 0.042 1614 Dihedral : 29.276 144.532 4323 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.45 % Allowed : 26.74 % 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 aren not related in a simple way. whole: 0.72 (0.28), residues: 913 helix: 1.55 (0.22), residues: 553 sheet: -3.63 (1.00), residues: 20 loop : -1.07 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 35 TYR 0.052 0.002 TYR D 80 PHE 0.012 0.001 PHE F 100 TRP 0.003 0.000 TRP K 21 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00573 (14550) covalent geometry : angle 0.63603 (20935) hydrogen bonds : bond 0.06409 ( 667) hydrogen bonds : angle 3.07131 ( 1658) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 264 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8909 (mm110) cc_final: 0.8661 (mm110) REVERT: B 98 TYR cc_start: 0.9151 (m-10) cc_final: 0.8646 (m-10) REVERT: C 15 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7669 (ptpp) REVERT: C 73 ASN cc_start: 0.8707 (t0) cc_final: 0.8317 (t0) REVERT: C 75 LYS cc_start: 0.9160 (mmtp) cc_final: 0.8861 (mmmm) REVERT: C 77 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7967 (tpp80) REVERT: C 100 VAL cc_start: 0.9528 (t) cc_final: 0.9036 (p) REVERT: D 39 TYR cc_start: 0.8184 (t80) cc_final: 0.7526 (t80) REVERT: D 48 ASP cc_start: 0.8962 (m-30) cc_final: 0.8554 (p0) REVERT: D 76 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.7923 (ttm-80) REVERT: D 91 ILE cc_start: 0.9017 (mm) cc_final: 0.8751 (mt) REVERT: F 35 ARG cc_start: 0.8893 (tpt-90) cc_final: 0.8644 (tpt-90) REVERT: F 84 MET cc_start: 0.8167 (mmm) cc_final: 0.7623 (mmm) REVERT: G 39 TYR cc_start: 0.9273 (m-80) cc_final: 0.8762 (m-80) REVERT: G 71 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8367 (ttp80) REVERT: G 90 ASP cc_start: 0.8401 (t70) cc_final: 0.7747 (t70) REVERT: G 92 GLU cc_start: 0.8841 (pm20) cc_final: 0.8502 (pm20) REVERT: H 68 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8718 (mm-30) REVERT: H 77 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8479 (mp) REVERT: H 84 SER cc_start: 0.9114 (m) cc_final: 0.8602 (p) REVERT: H 102 GLU cc_start: 0.8199 (tp30) cc_final: 0.6954 (tm-30) REVERT: K 16 LYS cc_start: 0.8604 (tppt) cc_final: 0.8163 (tptm) REVERT: K 70 LYS cc_start: 0.4731 (mmtm) cc_final: 0.4456 (mmtm) REVERT: A 42 ARG cc_start: 0.7752 (mmm-85) cc_final: 0.7465 (mmm-85) REVERT: A 85 GLN cc_start: 0.8703 (mt0) cc_final: 0.8355 (mt0) REVERT: A 90 MET cc_start: 0.8320 (mmm) cc_final: 0.8069 (mmt) REVERT: A 120 MET cc_start: 0.8580 (mtp) cc_final: 0.7978 (mtp) REVERT: A 123 ASP cc_start: 0.9181 (m-30) cc_final: 0.8823 (m-30) REVERT: E 54 TYR cc_start: 0.8998 (m-80) cc_final: 0.8478 (m-80) REVERT: E 105 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8874 (mm-30) outliers start: 43 outliers final: 38 residues processed: 279 average time/residue: 0.1141 time to fit residues: 43.7512 Evaluate side-chains 303 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 94 ASN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN E 39 HIS E 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.089130 restraints weight = 21866.763| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.76 r_work: 0.2838 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14550 Z= 0.175 Angle : 0.594 8.808 20935 Z= 0.343 Chirality : 0.036 0.198 2347 Planarity : 0.004 0.044 1614 Dihedral : 29.147 144.915 4323 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.82 % Allowed : 27.76 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.28), residues: 913 helix: 1.78 (0.23), residues: 553 sheet: -3.65 (0.98), residues: 20 loop : -1.05 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.044 0.002 TYR D 80 PHE 0.011 0.001 PHE E 67 TRP 0.002 0.000 TRP K 21 HIS 0.010 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00396 (14550) covalent geometry : angle 0.59387 (20935) hydrogen bonds : bond 0.05617 ( 667) hydrogen bonds : angle 2.86593 ( 1658) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8597 (ttt-90) REVERT: B 98 TYR cc_start: 0.9143 (m-10) cc_final: 0.8649 (m-10) REVERT: C 15 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7462 (mtmm) REVERT: C 61 GLU cc_start: 0.8792 (tp30) cc_final: 0.8466 (tp30) REVERT: C 73 ASN cc_start: 0.8626 (t0) cc_final: 0.8009 (t0) REVERT: C 75 LYS cc_start: 0.9095 (mmtp) cc_final: 0.8883 (mmmm) REVERT: C 77 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8075 (tpp80) REVERT: C 100 VAL cc_start: 0.9502 (t) cc_final: 0.9009 (p) REVERT: D 39 TYR cc_start: 0.8065 (t80) cc_final: 0.7435 (t80) REVERT: D 48 ASP cc_start: 0.8916 (m-30) cc_final: 0.8510 (p0) REVERT: D 76 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7894 (ttm-80) REVERT: D 91 ILE cc_start: 0.8974 (mm) cc_final: 0.8682 (mt) REVERT: F 35 ARG cc_start: 0.8822 (tpt-90) cc_final: 0.8563 (tpt-90) REVERT: F 52 GLU cc_start: 0.9168 (tp30) cc_final: 0.8352 (tp30) REVERT: F 84 MET cc_start: 0.8063 (mmm) cc_final: 0.7541 (mmm) REVERT: G 39 TYR cc_start: 0.9221 (m-80) cc_final: 0.8851 (m-80) REVERT: G 90 ASP cc_start: 0.8542 (t70) cc_final: 0.7904 (t70) REVERT: G 92 GLU cc_start: 0.8815 (pm20) cc_final: 0.8474 (pm20) REVERT: H 68 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8703 (mm-30) REVERT: H 84 SER cc_start: 0.9114 (m) cc_final: 0.8598 (p) REVERT: H 102 GLU cc_start: 0.8133 (tp30) cc_final: 0.7098 (tm-30) REVERT: K 16 LYS cc_start: 0.8665 (tppt) cc_final: 0.8207 (tptm) REVERT: K 70 LYS cc_start: 0.4637 (mmtm) cc_final: 0.4378 (mmtm) REVERT: A 42 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.7345 (mmm-85) REVERT: A 82 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8869 (mm) REVERT: A 85 GLN cc_start: 0.8690 (mt0) cc_final: 0.8309 (mt0) REVERT: A 90 MET cc_start: 0.8190 (mmm) cc_final: 0.7901 (mmt) REVERT: A 120 MET cc_start: 0.8542 (mtp) cc_final: 0.7940 (mtp) REVERT: A 123 ASP cc_start: 0.9173 (m-30) cc_final: 0.8833 (m-30) REVERT: E 54 TYR cc_start: 0.8836 (m-80) cc_final: 0.8302 (m-80) REVERT: E 105 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8901 (mm-30) outliers start: 38 outliers final: 32 residues processed: 283 average time/residue: 0.1151 time to fit residues: 44.1735 Evaluate side-chains 298 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 9 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN E 39 HIS E 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.089540 restraints weight = 21987.120| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.76 r_work: 0.2842 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14550 Z= 0.176 Angle : 0.591 8.828 20935 Z= 0.343 Chirality : 0.036 0.185 2347 Planarity : 0.004 0.042 1614 Dihedral : 29.126 144.622 4323 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.69 % Allowed : 28.39 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.28), residues: 913 helix: 1.84 (0.22), residues: 553 sheet: -3.64 (0.98), residues: 20 loop : -1.07 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.043 0.002 TYR D 80 PHE 0.011 0.001 PHE E 67 TRP 0.003 0.000 TRP K 21 HIS 0.007 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00398 (14550) covalent geometry : angle 0.59145 (20935) hydrogen bonds : bond 0.05600 ( 667) hydrogen bonds : angle 2.84890 ( 1658) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2926.31 seconds wall clock time: 50 minutes 29.25 seconds (3029.25 seconds total)