Starting phenix.real_space_refine on Wed Mar 4 09:43:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbq_16549/03_2026/8cbq_16549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbq_16549/03_2026/8cbq_16549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cbq_16549/03_2026/8cbq_16549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbq_16549/03_2026/8cbq_16549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cbq_16549/03_2026/8cbq_16549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbq_16549/03_2026/8cbq_16549.map" } resolution = 4.0 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 13 5.16 5 C 7231 2.51 5 N 2421 2.21 5 O 2994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12959 Number of models: 1 Model: "" Number of chains: 11 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} Time building chain proxies: 2.89, per 1000 atoms: 0.22 Number of scatterers: 12959 At special positions: 0 Unit cell: (135.792, 81.144, 120.888, 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 13 16.00 P 300 15.00 O 2994 8.00 N 2421 7.00 C 7231 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: 1.02 Conformation dependent library (CDL) restraints added in 407.2 milliseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 63.0% alpha, 4.2% beta 125 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 2.33 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: 3.791A 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: 3.868A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.646A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.515A 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: 3.541A 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: 3.585A 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: 3.735A 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: 3.542A 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: 3.525A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.764A 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: 3.944A 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: 3.749A 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: 3.656A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.515A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.516A 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: 3.798A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.585A 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: 3.957A 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: 3.733A 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: 5.136A 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: 3.658A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.571A 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: 3.622A 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: 3.683A 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: 3.544A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.152A 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: 6.433A 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: 7.167A 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) 351 hydrogen bonds defined for protein. 1035 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: 2.43 Time building geometry restraints manager: 1.45 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: 2280 1.33 - 1.45: 4689 1.45 - 1.57: 6221 1.57 - 1.69: 598 1.69 - 1.81: 26 Bond restraints: 13814 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 8.32e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.761 0.056 2.00e-02 2.50e+03 7.73e+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 6.55e+00 bond pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.15e+00 bond pdb=" CB ARG F 78 " pdb=" CG ARG F 78 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.40e+00 ... (remaining 13809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 18961 1.60 - 3.20: 914 3.20 - 4.79: 49 4.79 - 6.39: 12 6.39 - 7.99: 7 Bond angle restraints: 19943 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 120.20 125.91 -5.71 1.50e+00 4.44e-01 1.45e+01 angle pdb=" C SER K 62 " pdb=" N GLU K 63 " pdb=" CA GLU K 63 " ideal model delta sigma weight residual 122.61 128.15 -5.54 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 120.20 125.03 -4.83 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " pdb=" P DC I 35 " ideal model delta sigma weight residual 120.20 125.00 -4.80 1.50e+00 4.44e-01 1.03e+01 angle pdb=" CA GLU K 63 " pdb=" CB GLU K 63 " pdb=" CG GLU K 63 " ideal model delta sigma weight residual 114.10 119.63 -5.53 2.00e+00 2.50e-01 7.64e+00 ... (remaining 19938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 6151 34.28 - 68.56: 1376 68.56 - 102.84: 15 102.84 - 137.12: 2 137.12 - 171.39: 1 Dihedral angle restraints: 7545 sinusoidal: 5071 harmonic: 2474 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 48.61 171.39 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 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 7542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1240 0.035 - 0.070: 801 0.070 - 0.105: 162 0.105 - 0.140: 41 0.140 - 0.175: 9 Chirality restraints: 2253 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 7.68e-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 6.06e-01 chirality pdb=" CB VAL K 90 " pdb=" CA VAL K 90 " pdb=" CG1 VAL K 90 " pdb=" CG2 VAL K 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 2250 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO E 66 " 0.119 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 C 79 " -0.045 5.00e-02 4.00e+02 6.72e-02 7.22e+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 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+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 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3125 2.81 - 3.33: 10148 3.33 - 3.85: 23925 3.85 - 4.38: 31341 4.38 - 4.90: 43637 Nonbonded interactions: 112176 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.284 3.040 nonbonded pdb=" NH2 ARG H 83 " pdb=" OP2 DG J -33 " model vdw 2.330 3.120 nonbonded pdb=" O2 DC I -38 " pdb=" N2 DG J 38 " model vdw 2.359 3.120 nonbonded pdb=" NH2 ARG D 83 " pdb=" OP2 DA I -33 " model vdw 2.361 3.120 nonbonded pdb=" ND2 ASN B 25 " pdb=" OE1 GLU A 73 " model vdw 2.364 3.120 ... (remaining 112171 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 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 13814 Z= 0.370 Angle : 0.724 7.992 19943 Z= 0.428 Chirality : 0.044 0.175 2253 Planarity : 0.006 0.069 1485 Dihedral : 26.198 171.394 5947 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 7.99 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.85 (0.18), residues: 831 helix: -4.46 (0.09), residues: 530 sheet: -4.09 (0.99), residues: 17 loop : -2.11 (0.29), residues: 284 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 G 25 TRP 0.005 0.002 TRP K 82 HIS 0.004 0.001 HIS K 20 Details of bonding type rmsd covalent geometry : bond 0.00834 (13814) covalent geometry : angle 0.72447 (19943) hydrogen bonds : bond 0.31386 ( 658) hydrogen bonds : angle 10.64236 ( 1637) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 460 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8026 (mt) cc_final: 0.7415 (mt) REVERT: B 44 LYS cc_start: 0.8631 (tttt) cc_final: 0.8380 (mtmt) REVERT: B 53 GLU cc_start: 0.8302 (tp30) cc_final: 0.7386 (tp30) REVERT: C 32 ARG cc_start: 0.6931 (ttp80) cc_final: 0.6706 (ttp80) REVERT: C 62 ILE cc_start: 0.9381 (mt) cc_final: 0.9068 (mm) REVERT: C 68 ASN cc_start: 0.8832 (m-40) cc_final: 0.8231 (m-40) REVERT: C 83 LEU cc_start: 0.9336 (mt) cc_final: 0.8972 (mt) REVERT: C 87 VAL cc_start: 0.9403 (m) cc_final: 0.9124 (m) REVERT: C 110 ASN cc_start: 0.7942 (t0) cc_final: 0.7375 (t0) REVERT: D 49 THR cc_start: 0.8903 (m) cc_final: 0.8702 (m) REVERT: D 59 MET cc_start: 0.8965 (mmm) cc_final: 0.8372 (tpp) REVERT: D 110 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7295 (mt-10) REVERT: F 25 ASN cc_start: 0.8290 (m-40) cc_final: 0.7814 (m110) REVERT: F 34 ILE cc_start: 0.8857 (mt) cc_final: 0.8633 (mm) REVERT: F 39 ARG cc_start: 0.9036 (mmt-90) cc_final: 0.8787 (mmt180) REVERT: F 75 HIS cc_start: 0.7838 (t70) cc_final: 0.7611 (t70) REVERT: F 88 TYR cc_start: 0.8657 (m-10) cc_final: 0.8428 (m-80) REVERT: G 20 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7420 (mtt90) REVERT: G 57 TYR cc_start: 0.8128 (t80) cc_final: 0.7804 (t80) REVERT: G 110 ASN cc_start: 0.8643 (t0) cc_final: 0.8246 (t0) REVERT: H 110 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8303 (mt-10) REVERT: H 113 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8240 (tppt) REVERT: K 40 LEU cc_start: 0.2756 (OUTLIER) cc_final: 0.2391 (tp) REVERT: A 46 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8817 (t) REVERT: A 49 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7531 (mtp-110) REVERT: A 51 ILE cc_start: 0.8963 (mt) cc_final: 0.8737 (mt) REVERT: A 55 GLN cc_start: 0.8344 (mt0) cc_final: 0.7895 (mt0) REVERT: A 62 ILE cc_start: 0.8573 (mt) cc_final: 0.8240 (mt) REVERT: A 76 GLN cc_start: 0.8258 (mm110) cc_final: 0.7928 (mm-40) REVERT: A 84 PHE cc_start: 0.8420 (m-80) cc_final: 0.7629 (m-80) REVERT: A 99 TYR cc_start: 0.8300 (t80) cc_final: 0.8097 (t80) REVERT: A 120 MET cc_start: 0.7237 (mtp) cc_final: 0.6922 (mmm) REVERT: E 60 LEU cc_start: 0.8200 (mt) cc_final: 0.7431 (mp) REVERT: E 71 VAL cc_start: 0.9446 (t) cc_final: 0.9191 (t) REVERT: E 74 ILE cc_start: 0.9177 (mt) cc_final: 0.8909 (tt) REVERT: E 117 VAL cc_start: 0.9086 (t) cc_final: 0.8853 (p) REVERT: E 118 THR cc_start: 0.8515 (m) cc_final: 0.7808 (p) REVERT: E 119 ILE cc_start: 0.8810 (pt) cc_final: 0.7799 (pt) REVERT: E 120 MET cc_start: 0.7605 (mtt) cc_final: 0.6556 (mpp) outliers start: 13 outliers final: 6 residues processed: 468 average time/residue: 0.1840 time to fit residues: 110.3955 Evaluate side-chains 374 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 366 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.0570 chunk 106 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 64 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS G 89 ASN H 46 HIS H 64 ASN H 92 GLN K 64 ASN K 86 ASN A 85 GLN A 108 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.147745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.106201 restraints weight = 28887.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109765 restraints weight = 14944.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112086 restraints weight = 9893.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.113558 restraints weight = 7649.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.114434 restraints weight = 6543.978| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 13814 Z= 0.197 Angle : 0.712 7.771 19943 Z= 0.409 Chirality : 0.039 0.206 2253 Planarity : 0.007 0.086 1485 Dihedral : 29.795 157.264 4250 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.63 % Allowed : 23.00 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.24), residues: 831 helix: -1.74 (0.19), residues: 525 sheet: -4.30 (1.23), residues: 10 loop : -1.36 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 129 TYR 0.022 0.002 TYR F 51 PHE 0.020 0.002 PHE H 62 TRP 0.003 0.000 TRP K 82 HIS 0.007 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00441 (13814) covalent geometry : angle 0.71160 (19943) hydrogen bonds : bond 0.06419 ( 658) hydrogen bonds : angle 3.49598 ( 1637) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 404 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8676 (m110) cc_final: 0.8411 (m110) REVERT: B 44 LYS cc_start: 0.9029 (tttt) cc_final: 0.8753 (mtpp) REVERT: B 79 LYS cc_start: 0.8889 (mmtp) cc_final: 0.8392 (mmtm) REVERT: C 32 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7327 (ttp80) REVERT: C 71 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7091 (ttp-110) REVERT: C 75 LYS cc_start: 0.8430 (mmmm) cc_final: 0.7996 (mmmm) REVERT: C 95 LYS cc_start: 0.9118 (ptpt) cc_final: 0.8836 (pttp) REVERT: C 110 ASN cc_start: 0.8930 (t0) cc_final: 0.8430 (t0) REVERT: C 115 LEU cc_start: 0.9275 (mt) cc_final: 0.9016 (mp) REVERT: D 34 TYR cc_start: 0.8620 (m-80) cc_final: 0.8254 (m-10) REVERT: D 49 THR cc_start: 0.8509 (m) cc_final: 0.8155 (p) REVERT: D 59 MET cc_start: 0.9723 (mmm) cc_final: 0.9205 (tpp) REVERT: D 64 ASN cc_start: 0.8829 (m110) cc_final: 0.8317 (m110) REVERT: D 65 ASP cc_start: 0.8812 (t70) cc_final: 0.8401 (t70) REVERT: D 105 LYS cc_start: 0.8631 (tptp) cc_final: 0.8371 (tptp) REVERT: D 110 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7685 (mt-10) REVERT: D 113 LYS cc_start: 0.9070 (mmtm) cc_final: 0.8751 (mmtm) REVERT: D 117 LYS cc_start: 0.9208 (tttt) cc_final: 0.8963 (ptmt) REVERT: F 25 ASN cc_start: 0.8580 (m-40) cc_final: 0.8036 (m-40) REVERT: F 39 ARG cc_start: 0.9127 (mmt-90) cc_final: 0.8621 (mmt180) REVERT: F 53 GLU cc_start: 0.8547 (tp30) cc_final: 0.7776 (tp30) REVERT: F 75 HIS cc_start: 0.8334 (t70) cc_final: 0.7896 (t70) REVERT: F 79 LYS cc_start: 0.9026 (mmtm) cc_final: 0.8769 (mmtm) REVERT: F 88 TYR cc_start: 0.9188 (m-10) cc_final: 0.8693 (m-80) REVERT: F 92 ARG cc_start: 0.8963 (mmm160) cc_final: 0.8738 (mmm-85) REVERT: F 95 ARG cc_start: 0.8323 (mpp80) cc_final: 0.8118 (mtt90) REVERT: G 20 ARG cc_start: 0.8480 (mtt90) cc_final: 0.7606 (mtt-85) REVERT: G 42 ARG cc_start: 0.8534 (mtp-110) cc_final: 0.8038 (mtm-85) REVERT: G 61 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8063 (mm-30) REVERT: G 73 ASN cc_start: 0.8746 (t0) cc_final: 0.8218 (t0) REVERT: G 81 ARG cc_start: 0.8549 (tpt90) cc_final: 0.8344 (tpt90) REVERT: G 92 GLU cc_start: 0.8616 (pm20) cc_final: 0.8406 (pm20) REVERT: G 110 ASN cc_start: 0.8969 (t0) cc_final: 0.8420 (t0) REVERT: G 112 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8268 (mm110) REVERT: H 34 TYR cc_start: 0.8109 (m-80) cc_final: 0.7551 (m-10) REVERT: H 39 TYR cc_start: 0.8293 (t80) cc_final: 0.7990 (t80) REVERT: H 40 LYS cc_start: 0.8859 (tppt) cc_final: 0.8435 (tppt) REVERT: H 43 LYS cc_start: 0.8542 (pptt) cc_final: 0.7927 (pptt) REVERT: H 44 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8294 (mm-40) REVERT: H 102 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8361 (mm-30) REVERT: H 113 LYS cc_start: 0.9313 (mtmt) cc_final: 0.9008 (ptpt) REVERT: K 40 LEU cc_start: 0.4451 (OUTLIER) cc_final: 0.3981 (tp) REVERT: A 40 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7805 (mtp180) REVERT: A 55 GLN cc_start: 0.9266 (mt0) cc_final: 0.8815 (tt0) REVERT: A 56 LYS cc_start: 0.8467 (pttp) cc_final: 0.8165 (ptpp) REVERT: A 72 ARG cc_start: 0.8907 (mtt-85) cc_final: 0.8530 (mtt-85) REVERT: A 76 GLN cc_start: 0.8680 (mm110) cc_final: 0.8172 (mm-40) REVERT: A 79 LYS cc_start: 0.8779 (tptp) cc_final: 0.8163 (tptt) REVERT: A 106 ASP cc_start: 0.8797 (m-30) cc_final: 0.8530 (m-30) REVERT: A 129 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8140 (mmp80) REVERT: E 41 TYR cc_start: 0.8146 (m-80) cc_final: 0.7552 (m-80) REVERT: E 49 ARG cc_start: 0.8505 (ptm160) cc_final: 0.8014 (ptp-170) REVERT: E 50 GLU cc_start: 0.8258 (pt0) cc_final: 0.7631 (pt0) REVERT: E 68 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7754 (pp30) REVERT: E 71 VAL cc_start: 0.9108 (t) cc_final: 0.8855 (t) REVERT: E 85 GLN cc_start: 0.7932 (mt0) cc_final: 0.7539 (mt0) REVERT: E 105 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7519 (tm-30) REVERT: E 117 VAL cc_start: 0.9172 (t) cc_final: 0.8890 (p) REVERT: E 119 ILE cc_start: 0.9018 (pt) cc_final: 0.8047 (pt) REVERT: E 120 MET cc_start: 0.6732 (mtt) cc_final: 0.6309 (mpp) REVERT: E 125 GLN cc_start: 0.8719 (mt0) cc_final: 0.8414 (mm-40) REVERT: E 129 ARG cc_start: 0.8930 (mmm160) cc_final: 0.8376 (mmm-85) outliers start: 33 outliers final: 20 residues processed: 416 average time/residue: 0.1675 time to fit residues: 90.6585 Evaluate side-chains 391 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 370 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 0.1980 chunk 108 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 29 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 89 ASN D 46 HIS G 89 ASN H 92 GLN H 106 HIS A 85 GLN A 108 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 108 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.144518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.100194 restraints weight = 29274.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103513 restraints weight = 15700.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105630 restraints weight = 10693.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.106997 restraints weight = 8463.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.107799 restraints weight = 7338.941| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13814 Z= 0.166 Angle : 0.661 11.135 19943 Z= 0.376 Chirality : 0.036 0.204 2253 Planarity : 0.005 0.061 1485 Dihedral : 29.627 154.068 4242 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.49 % Allowed : 27.77 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.27), residues: 831 helix: -0.08 (0.22), residues: 533 sheet: -4.11 (1.22), residues: 10 loop : -1.21 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 32 TYR 0.013 0.001 TYR C 50 PHE 0.013 0.002 PHE F 61 TRP 0.003 0.000 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00373 (13814) covalent geometry : angle 0.66122 (19943) hydrogen bonds : bond 0.05435 ( 658) hydrogen bonds : angle 3.16342 ( 1637) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 398 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9242 (mtp85) cc_final: 0.8653 (mtp85) REVERT: B 45 ARG cc_start: 0.8991 (mtp-110) cc_final: 0.8616 (ttp80) REVERT: B 63 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7645 (mt-10) REVERT: B 79 LYS cc_start: 0.8968 (mmtp) cc_final: 0.8766 (mmtp) REVERT: C 32 ARG cc_start: 0.7864 (ttp80) cc_final: 0.6732 (ttp-170) REVERT: C 36 LYS cc_start: 0.8681 (pttm) cc_final: 0.8448 (pttm) REVERT: C 71 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7471 (ttp-110) REVERT: C 91 GLU cc_start: 0.8481 (pm20) cc_final: 0.7923 (pm20) REVERT: C 95 LYS cc_start: 0.9209 (ptpt) cc_final: 0.8741 (pttt) REVERT: C 110 ASN cc_start: 0.8970 (t0) cc_final: 0.8565 (t0) REVERT: C 116 LEU cc_start: 0.8920 (tp) cc_final: 0.8658 (mt) REVERT: D 49 THR cc_start: 0.8422 (m) cc_final: 0.8142 (p) REVERT: D 59 MET cc_start: 0.9731 (mmm) cc_final: 0.9436 (tpp) REVERT: D 64 ASN cc_start: 0.8707 (m-40) cc_final: 0.8318 (m110) REVERT: D 65 ASP cc_start: 0.8847 (t70) cc_final: 0.8496 (t70) REVERT: D 92 GLN cc_start: 0.8106 (pt0) cc_final: 0.7700 (pp30) REVERT: D 102 GLU cc_start: 0.8129 (tp30) cc_final: 0.7595 (tp30) REVERT: D 109 SER cc_start: 0.9366 (t) cc_final: 0.8888 (p) REVERT: D 110 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7855 (mt-10) REVERT: F 25 ASN cc_start: 0.8622 (m-40) cc_final: 0.8338 (m-40) REVERT: F 36 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.7402 (mtm-85) REVERT: F 53 GLU cc_start: 0.8492 (tp30) cc_final: 0.7713 (tp30) REVERT: F 75 HIS cc_start: 0.8301 (t70) cc_final: 0.7958 (t70) REVERT: F 79 LYS cc_start: 0.9005 (mmtm) cc_final: 0.8641 (mmtm) REVERT: F 88 TYR cc_start: 0.9291 (m-10) cc_final: 0.8867 (m-80) REVERT: F 95 ARG cc_start: 0.8365 (mpp80) cc_final: 0.8081 (mtt90) REVERT: G 17 ARG cc_start: 0.8279 (ptp-170) cc_final: 0.7559 (ptp-110) REVERT: G 39 TYR cc_start: 0.9122 (m-80) cc_final: 0.8649 (m-80) REVERT: G 58 LEU cc_start: 0.8585 (mt) cc_final: 0.8240 (mp) REVERT: G 61 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8194 (mm-30) REVERT: G 64 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7644 (tm-30) REVERT: G 68 ASN cc_start: 0.8419 (p0) cc_final: 0.7902 (p0) REVERT: G 72 ASP cc_start: 0.7679 (m-30) cc_final: 0.7444 (m-30) REVERT: G 78 ILE cc_start: 0.8478 (mt) cc_final: 0.8054 (mt) REVERT: G 81 ARG cc_start: 0.8740 (tpt90) cc_final: 0.8484 (tpt90) REVERT: G 95 LYS cc_start: 0.9140 (pttp) cc_final: 0.8697 (pttm) REVERT: H 34 TYR cc_start: 0.8087 (m-80) cc_final: 0.7690 (m-10) REVERT: H 40 LYS cc_start: 0.9515 (tppt) cc_final: 0.9130 (tppt) REVERT: H 56 MET cc_start: 0.8020 (tmm) cc_final: 0.7765 (tmm) REVERT: H 59 MET cc_start: 0.9162 (mmp) cc_final: 0.8810 (mmp) REVERT: H 99 LEU cc_start: 0.9109 (mp) cc_final: 0.8896 (mt) REVERT: H 102 GLU cc_start: 0.9027 (mm-30) cc_final: 0.7978 (mm-30) REVERT: K 40 LEU cc_start: 0.4732 (OUTLIER) cc_final: 0.4373 (tp) REVERT: A 76 GLN cc_start: 0.8672 (mm110) cc_final: 0.8285 (mm-40) REVERT: E 41 TYR cc_start: 0.8223 (m-80) cc_final: 0.7962 (m-80) REVERT: E 49 ARG cc_start: 0.8474 (ptm160) cc_final: 0.7945 (ptp90) REVERT: E 50 GLU cc_start: 0.8093 (pt0) cc_final: 0.7781 (pt0) REVERT: E 56 LYS cc_start: 0.8045 (mmtm) cc_final: 0.7680 (mmtm) REVERT: E 68 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7994 (pp30) REVERT: E 85 GLN cc_start: 0.8267 (mt0) cc_final: 0.7476 (mt0) REVERT: E 105 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7559 (tm-30) REVERT: E 117 VAL cc_start: 0.9272 (t) cc_final: 0.9022 (p) REVERT: E 120 MET cc_start: 0.7068 (mtt) cc_final: 0.6524 (mpp) REVERT: E 125 GLN cc_start: 0.8731 (mt0) cc_final: 0.8397 (mm-40) outliers start: 32 outliers final: 23 residues processed: 410 average time/residue: 0.1603 time to fit residues: 85.8260 Evaluate side-chains 402 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 377 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN K 78 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.142373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099024 restraints weight = 29217.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.102297 restraints weight = 15554.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.104343 restraints weight = 10544.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.105619 restraints weight = 8335.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106359 restraints weight = 7271.600| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13814 Z= 0.166 Angle : 0.650 13.854 19943 Z= 0.369 Chirality : 0.036 0.225 2253 Planarity : 0.005 0.060 1485 Dihedral : 29.509 152.087 4239 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.75 % Allowed : 30.01 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.28), residues: 831 helix: 0.54 (0.22), residues: 533 sheet: -3.73 (1.45), residues: 10 loop : -0.94 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 35 TYR 0.018 0.002 TYR F 51 PHE 0.027 0.002 PHE B 61 TRP 0.003 0.000 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00375 (13814) covalent geometry : angle 0.65012 (19943) hydrogen bonds : bond 0.05172 ( 658) hydrogen bonds : angle 3.13103 ( 1637) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 391 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9166 (mtp85) cc_final: 0.8856 (mtp85) REVERT: B 45 ARG cc_start: 0.9022 (mtp-110) cc_final: 0.8610 (mtp85) REVERT: B 63 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7724 (mt-10) REVERT: B 95 ARG cc_start: 0.7292 (mmm-85) cc_final: 0.6981 (mmm-85) REVERT: C 24 GLN cc_start: 0.8777 (mm-40) cc_final: 0.7934 (mm-40) REVERT: C 29 ARG cc_start: 0.8566 (tpp80) cc_final: 0.7469 (tpp80) REVERT: C 32 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7484 (ttp-110) REVERT: C 42 ARG cc_start: 0.8629 (mtm-85) cc_final: 0.8315 (mtm-85) REVERT: C 71 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7702 (ttp-110) REVERT: C 75 LYS cc_start: 0.9084 (mmtm) cc_final: 0.8715 (mmmm) REVERT: C 89 ASN cc_start: 0.8649 (m-40) cc_final: 0.8276 (m110) REVERT: C 110 ASN cc_start: 0.8970 (t0) cc_final: 0.8590 (t0) REVERT: D 31 LYS cc_start: 0.8338 (mppt) cc_final: 0.8132 (mppt) REVERT: D 49 THR cc_start: 0.8633 (m) cc_final: 0.8264 (p) REVERT: D 59 MET cc_start: 0.9726 (mmm) cc_final: 0.9454 (tpp) REVERT: D 64 ASN cc_start: 0.8653 (m-40) cc_final: 0.8275 (m110) REVERT: D 69 ARG cc_start: 0.8729 (mmm-85) cc_final: 0.8497 (mtp180) REVERT: D 73 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8945 (mm-30) REVERT: D 92 GLN cc_start: 0.8190 (pt0) cc_final: 0.7793 (pp30) REVERT: D 102 GLU cc_start: 0.7937 (tp30) cc_final: 0.7552 (tp30) REVERT: D 109 SER cc_start: 0.9402 (t) cc_final: 0.8737 (p) REVERT: D 110 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8022 (mt-10) REVERT: D 113 LYS cc_start: 0.9256 (mtmm) cc_final: 0.8938 (mmtm) REVERT: D 117 LYS cc_start: 0.9301 (tttt) cc_final: 0.8950 (ptmt) REVERT: F 31 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8731 (tptt) REVERT: F 44 LYS cc_start: 0.9026 (mtmm) cc_final: 0.8720 (mttp) REVERT: F 53 GLU cc_start: 0.8493 (tp30) cc_final: 0.7796 (tp30) REVERT: F 67 ARG cc_start: 0.8933 (ttp80) cc_final: 0.8654 (ttp80) REVERT: F 70 VAL cc_start: 0.9211 (t) cc_final: 0.8999 (p) REVERT: F 75 HIS cc_start: 0.8453 (t70) cc_final: 0.8057 (t70) REVERT: F 78 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7828 (tpp80) REVERT: F 79 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8721 (mmtm) REVERT: F 88 TYR cc_start: 0.9318 (m-10) cc_final: 0.8884 (m-80) REVERT: F 90 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9062 (mp) REVERT: F 95 ARG cc_start: 0.8301 (mpp80) cc_final: 0.7964 (mtt90) REVERT: G 17 ARG cc_start: 0.8411 (ptp-170) cc_final: 0.7591 (ptp-170) REVERT: G 39 TYR cc_start: 0.9118 (m-80) cc_final: 0.8843 (m-80) REVERT: G 42 ARG cc_start: 0.8463 (mtm180) cc_final: 0.7384 (mtm180) REVERT: G 61 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8266 (mm-30) REVERT: G 64 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7655 (tm-30) REVERT: G 68 ASN cc_start: 0.8500 (p0) cc_final: 0.7959 (p0) REVERT: G 81 ARG cc_start: 0.8874 (tpt90) cc_final: 0.8574 (tpt90) REVERT: G 84 GLN cc_start: 0.9420 (tp-100) cc_final: 0.9213 (tp-100) REVERT: G 95 LYS cc_start: 0.9185 (pttp) cc_final: 0.8790 (pttm) REVERT: H 34 TYR cc_start: 0.8218 (m-80) cc_final: 0.7751 (m-10) REVERT: H 40 LYS cc_start: 0.9403 (tppt) cc_final: 0.8972 (tptt) REVERT: H 43 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8235 (ptpt) REVERT: H 56 MET cc_start: 0.8088 (tmm) cc_final: 0.7794 (tmm) REVERT: H 59 MET cc_start: 0.9259 (mmp) cc_final: 0.8889 (mmp) REVERT: H 102 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8226 (mm-30) REVERT: H 105 LYS cc_start: 0.9232 (ptmm) cc_final: 0.8696 (pttm) REVERT: A 76 GLN cc_start: 0.8846 (mm110) cc_final: 0.8445 (mm-40) REVERT: E 39 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6861 (p-80) REVERT: E 50 GLU cc_start: 0.8170 (pt0) cc_final: 0.7966 (pt0) REVERT: E 53 ARG cc_start: 0.8555 (tpt90) cc_final: 0.8265 (tpt90) REVERT: E 56 LYS cc_start: 0.8212 (mmtm) cc_final: 0.7836 (mmtm) REVERT: E 73 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: E 81 ASP cc_start: 0.8371 (m-30) cc_final: 0.8081 (m-30) REVERT: E 85 GLN cc_start: 0.8244 (mt0) cc_final: 0.7971 (mt0) REVERT: E 93 GLN cc_start: 0.7435 (tm-30) cc_final: 0.6641 (tm-30) REVERT: E 105 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7562 (tm-30) REVERT: E 117 VAL cc_start: 0.9402 (t) cc_final: 0.9150 (p) REVERT: E 119 ILE cc_start: 0.8751 (pt) cc_final: 0.7436 (pt) REVERT: E 120 MET cc_start: 0.7222 (mtt) cc_final: 0.6870 (mpp) REVERT: E 125 GLN cc_start: 0.8733 (mt0) cc_final: 0.8440 (mm-40) outliers start: 41 outliers final: 23 residues processed: 405 average time/residue: 0.1613 time to fit residues: 85.4867 Evaluate side-chains 406 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 379 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN G 89 ASN A 108 ASN A 125 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.138283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095643 restraints weight = 30644.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.098686 restraints weight = 16829.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100656 restraints weight = 11670.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101879 restraints weight = 9303.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102553 restraints weight = 8131.111| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 13814 Z= 0.219 Angle : 0.681 14.112 19943 Z= 0.387 Chirality : 0.038 0.198 2253 Planarity : 0.005 0.060 1485 Dihedral : 29.596 149.900 4237 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 6.87 % Allowed : 31.28 % Favored : 61.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.28), residues: 831 helix: 0.78 (0.22), residues: 531 sheet: -3.59 (1.46), residues: 10 loop : -0.81 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 35 TYR 0.023 0.002 TYR F 51 PHE 0.029 0.002 PHE F 61 TRP 0.003 0.001 TRP K 82 HIS 0.005 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00499 (13814) covalent geometry : angle 0.68074 (19943) hydrogen bonds : bond 0.05657 ( 658) hydrogen bonds : angle 3.40635 ( 1637) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 391 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9174 (mtp85) cc_final: 0.8792 (ttm110) REVERT: B 45 ARG cc_start: 0.9134 (mtp-110) cc_final: 0.8867 (mtp85) REVERT: B 55 ARG cc_start: 0.8600 (mtt90) cc_final: 0.8340 (ttm110) REVERT: B 63 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7720 (mt-10) REVERT: B 78 ARG cc_start: 0.8716 (ttp-110) cc_final: 0.8484 (mtp85) REVERT: B 79 LYS cc_start: 0.9357 (mmmm) cc_final: 0.8901 (mmmm) REVERT: B 82 THR cc_start: 0.8834 (p) cc_final: 0.8548 (t) REVERT: B 95 ARG cc_start: 0.6850 (mmm-85) cc_final: 0.6519 (mmm-85) REVERT: C 20 ARG cc_start: 0.8767 (mmt-90) cc_final: 0.8534 (mpt-90) REVERT: C 24 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8198 (mm-40) REVERT: C 29 ARG cc_start: 0.7997 (tpp80) cc_final: 0.5218 (tpp80) REVERT: C 32 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7001 (ttp-170) REVERT: C 34 LEU cc_start: 0.8707 (mt) cc_final: 0.8462 (mt) REVERT: C 71 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7668 (ttp-110) REVERT: C 84 GLN cc_start: 0.9264 (tp-100) cc_final: 0.9003 (tp-100) REVERT: C 89 ASN cc_start: 0.8672 (m-40) cc_final: 0.8267 (m-40) REVERT: C 110 ASN cc_start: 0.9129 (t0) cc_final: 0.8813 (t0) REVERT: C 115 LEU cc_start: 0.8963 (mt) cc_final: 0.8519 (mm) REVERT: D 31 LYS cc_start: 0.8502 (mppt) cc_final: 0.8191 (mppt) REVERT: D 64 ASN cc_start: 0.8760 (m-40) cc_final: 0.8192 (m-40) REVERT: D 92 GLN cc_start: 0.8132 (pt0) cc_final: 0.7750 (pp30) REVERT: D 105 LYS cc_start: 0.8512 (tptp) cc_final: 0.8265 (tptp) REVERT: D 109 SER cc_start: 0.9482 (t) cc_final: 0.8880 (p) REVERT: D 113 LYS cc_start: 0.9227 (mtmm) cc_final: 0.8921 (mtmm) REVERT: F 31 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8548 (ttmt) REVERT: F 51 TYR cc_start: 0.8589 (m-10) cc_final: 0.8081 (m-10) REVERT: F 53 GLU cc_start: 0.8490 (tp30) cc_final: 0.8069 (tp30) REVERT: F 70 VAL cc_start: 0.9263 (t) cc_final: 0.9062 (p) REVERT: F 74 GLU cc_start: 0.8413 (tp30) cc_final: 0.8075 (tp30) REVERT: F 79 LYS cc_start: 0.8985 (mmtm) cc_final: 0.8541 (mmtm) REVERT: F 88 TYR cc_start: 0.9403 (m-10) cc_final: 0.8778 (m-80) REVERT: F 90 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9101 (mp) REVERT: F 95 ARG cc_start: 0.8629 (mpp80) cc_final: 0.8304 (mtt90) REVERT: G 18 SER cc_start: 0.9045 (m) cc_final: 0.8777 (t) REVERT: G 39 TYR cc_start: 0.9168 (m-80) cc_final: 0.8954 (m-80) REVERT: G 42 ARG cc_start: 0.8540 (mtm180) cc_final: 0.7914 (mtm180) REVERT: G 61 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8110 (mm-30) REVERT: G 68 ASN cc_start: 0.8411 (p0) cc_final: 0.7914 (p0) REVERT: G 92 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8130 (mm-30) REVERT: G 95 LYS cc_start: 0.9036 (pttp) cc_final: 0.8702 (pttm) REVERT: G 112 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8417 (mm110) REVERT: H 29 THR cc_start: 0.8487 (t) cc_final: 0.8225 (m) REVERT: H 48 ASP cc_start: 0.8641 (m-30) cc_final: 0.8205 (p0) REVERT: H 113 LYS cc_start: 0.9275 (mtmt) cc_final: 0.8958 (ptpt) REVERT: H 117 LYS cc_start: 0.9171 (tppt) cc_final: 0.8785 (tptp) REVERT: A 76 GLN cc_start: 0.8802 (mm110) cc_final: 0.8524 (mm-40) REVERT: E 39 HIS cc_start: 0.7614 (p-80) cc_final: 0.7243 (p-80) REVERT: E 55 GLN cc_start: 0.8505 (pt0) cc_final: 0.8150 (pt0) REVERT: E 56 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8116 (mmtm) REVERT: E 65 LEU cc_start: 0.8710 (tt) cc_final: 0.8098 (tt) REVERT: E 68 GLN cc_start: 0.8237 (pp30) cc_final: 0.7924 (pp30) REVERT: E 73 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8088 (tp30) REVERT: E 76 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8716 (tm-30) REVERT: E 81 ASP cc_start: 0.8570 (m-30) cc_final: 0.8250 (m-30) REVERT: E 85 GLN cc_start: 0.8711 (mt0) cc_final: 0.8398 (mt0) REVERT: E 87 SER cc_start: 0.9327 (OUTLIER) cc_final: 0.9079 (p) REVERT: E 90 MET cc_start: 0.9309 (mmm) cc_final: 0.9094 (mmp) REVERT: E 93 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7693 (tm-30) REVERT: E 97 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8264 (mt-10) REVERT: E 105 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7516 (tm-30) REVERT: E 115 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8584 (mmmm) REVERT: E 117 VAL cc_start: 0.9394 (t) cc_final: 0.9147 (p) outliers start: 49 outliers final: 33 residues processed: 405 average time/residue: 0.1581 time to fit residues: 83.8260 Evaluate side-chains 421 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 385 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 64 ASN G 73 ASN G 89 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.138423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095579 restraints weight = 30393.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098644 restraints weight = 16764.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.100633 restraints weight = 11623.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.101863 restraints weight = 9260.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.102595 restraints weight = 8086.987| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13814 Z= 0.184 Angle : 0.668 12.210 19943 Z= 0.376 Chirality : 0.037 0.210 2253 Planarity : 0.005 0.059 1485 Dihedral : 29.658 150.309 4237 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 6.45 % Allowed : 34.08 % Favored : 59.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.28), residues: 831 helix: 0.99 (0.22), residues: 532 sheet: -3.50 (1.49), residues: 10 loop : -0.74 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 83 TYR 0.021 0.001 TYR H 118 PHE 0.024 0.002 PHE B 61 TRP 0.002 0.000 TRP K 82 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00420 (13814) covalent geometry : angle 0.66824 (19943) hydrogen bonds : bond 0.05127 ( 658) hydrogen bonds : angle 3.29811 ( 1637) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 389 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ARG cc_start: 0.9062 (mtp-110) cc_final: 0.8856 (mtp85) REVERT: B 55 ARG cc_start: 0.8630 (mtt90) cc_final: 0.8335 (ttm110) REVERT: B 63 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 79 LYS cc_start: 0.9369 (mmmm) cc_final: 0.8919 (mmmm) REVERT: B 82 THR cc_start: 0.8874 (p) cc_final: 0.8466 (t) REVERT: B 88 TYR cc_start: 0.8897 (m-10) cc_final: 0.7832 (m-10) REVERT: B 95 ARG cc_start: 0.7158 (mmm-85) cc_final: 0.6940 (mmm-85) REVERT: C 20 ARG cc_start: 0.8811 (mmt-90) cc_final: 0.8494 (mpt-90) REVERT: C 24 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8210 (mm-40) REVERT: C 29 ARG cc_start: 0.8020 (tpp80) cc_final: 0.5966 (tpp80) REVERT: C 32 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7087 (ttp-170) REVERT: C 71 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7770 (ttp-110) REVERT: C 73 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8707 (t0) REVERT: C 89 ASN cc_start: 0.8639 (m-40) cc_final: 0.8225 (m110) REVERT: C 110 ASN cc_start: 0.9163 (t0) cc_final: 0.8928 (t0) REVERT: D 31 LYS cc_start: 0.8485 (mppt) cc_final: 0.8066 (mmtm) REVERT: D 64 ASN cc_start: 0.8681 (m-40) cc_final: 0.8130 (m-40) REVERT: D 73 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8742 (mm-30) REVERT: D 76 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8250 (ttp-110) REVERT: D 92 GLN cc_start: 0.8394 (pt0) cc_final: 0.7631 (pp30) REVERT: D 105 LYS cc_start: 0.8449 (tptp) cc_final: 0.7964 (tptp) REVERT: D 109 SER cc_start: 0.9447 (t) cc_final: 0.8705 (p) REVERT: D 113 LYS cc_start: 0.9252 (mtmm) cc_final: 0.8919 (mmtm) REVERT: F 31 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8592 (ttmt) REVERT: F 63 GLU cc_start: 0.7621 (pp20) cc_final: 0.7053 (pp20) REVERT: F 70 VAL cc_start: 0.9060 (t) cc_final: 0.8798 (p) REVERT: F 79 LYS cc_start: 0.8986 (mmtm) cc_final: 0.8601 (mmtm) REVERT: F 88 TYR cc_start: 0.9365 (m-10) cc_final: 0.8800 (m-80) REVERT: F 90 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9130 (mp) REVERT: F 95 ARG cc_start: 0.8632 (mpp80) cc_final: 0.8223 (mtt90) REVERT: G 18 SER cc_start: 0.9082 (m) cc_final: 0.8787 (t) REVERT: G 42 ARG cc_start: 0.8712 (mtm180) cc_final: 0.8305 (mtm180) REVERT: G 61 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8118 (mm-30) REVERT: G 79 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8428 (mm) REVERT: G 81 ARG cc_start: 0.9120 (tpt90) cc_final: 0.8540 (tpt90) REVERT: G 85 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9032 (mt) REVERT: G 89 ASN cc_start: 0.8562 (m-40) cc_final: 0.8089 (m110) REVERT: G 112 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8429 (mm110) REVERT: H 40 LYS cc_start: 0.9001 (tmtt) cc_final: 0.8753 (tptt) REVERT: H 48 ASP cc_start: 0.8573 (m-30) cc_final: 0.8210 (p0) REVERT: H 73 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8206 (mm-30) REVERT: H 113 LYS cc_start: 0.9248 (mtmt) cc_final: 0.8984 (tptt) REVERT: H 118 TYR cc_start: 0.8262 (t80) cc_final: 0.7510 (t80) REVERT: A 49 ARG cc_start: 0.8771 (mtp-110) cc_final: 0.8521 (mtp-110) REVERT: A 76 GLN cc_start: 0.8785 (mm110) cc_final: 0.8558 (mm-40) REVERT: E 39 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.7373 (p-80) REVERT: E 53 ARG cc_start: 0.8327 (tpt90) cc_final: 0.8024 (ttp80) REVERT: E 56 LYS cc_start: 0.8567 (mmtm) cc_final: 0.8112 (mmtm) REVERT: E 60 LEU cc_start: 0.9167 (mm) cc_final: 0.8937 (mm) REVERT: E 65 LEU cc_start: 0.8805 (tt) cc_final: 0.8067 (tt) REVERT: E 68 GLN cc_start: 0.8322 (pp30) cc_final: 0.7858 (pp30) REVERT: E 73 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8066 (tp30) REVERT: E 76 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8780 (tm-30) REVERT: E 85 GLN cc_start: 0.8752 (mt0) cc_final: 0.8454 (mt0) REVERT: E 87 SER cc_start: 0.9272 (m) cc_final: 0.9009 (p) REVERT: E 94 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8380 (mt-10) REVERT: E 97 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7439 (mt-10) REVERT: E 105 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7494 (tm-30) REVERT: E 115 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8573 (mmmm) REVERT: E 117 VAL cc_start: 0.9379 (t) cc_final: 0.9139 (p) outliers start: 46 outliers final: 34 residues processed: 403 average time/residue: 0.1631 time to fit residues: 85.6947 Evaluate side-chains 417 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 376 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 77 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.5980 chunk 106 optimal weight: 0.0370 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 75 HIS G 73 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.139644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097095 restraints weight = 30686.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100188 restraints weight = 16838.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.102190 restraints weight = 11645.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.103403 restraints weight = 9267.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.104176 restraints weight = 8094.211| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13814 Z= 0.167 Angle : 0.668 14.689 19943 Z= 0.374 Chirality : 0.036 0.210 2253 Planarity : 0.005 0.061 1485 Dihedral : 29.602 149.759 4237 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.77 % Allowed : 36.89 % Favored : 58.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.28), residues: 831 helix: 1.12 (0.22), residues: 528 sheet: -3.41 (1.51), residues: 10 loop : -0.67 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 35 TYR 0.037 0.002 TYR D 80 PHE 0.028 0.002 PHE B 61 TRP 0.002 0.000 TRP K 82 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00376 (13814) covalent geometry : angle 0.66770 (19943) hydrogen bonds : bond 0.04958 ( 658) hydrogen bonds : angle 3.18265 ( 1637) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 387 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 PRO cc_start: 0.9295 (Cg_exo) cc_final: 0.8998 (Cg_endo) REVERT: B 40 ARG cc_start: 0.9094 (tpp80) cc_final: 0.8885 (tpt-90) REVERT: B 45 ARG cc_start: 0.9079 (mtp-110) cc_final: 0.8789 (mtp85) REVERT: B 55 ARG cc_start: 0.8617 (mtt90) cc_final: 0.8286 (ttm110) REVERT: B 79 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8765 (mmmm) REVERT: C 17 ARG cc_start: 0.8892 (mtm180) cc_final: 0.8574 (mtt90) REVERT: C 20 ARG cc_start: 0.8813 (mmt-90) cc_final: 0.8469 (mpt-90) REVERT: C 24 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8254 (mm-40) REVERT: C 29 ARG cc_start: 0.7976 (tpp80) cc_final: 0.5888 (tpp80) REVERT: C 32 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7227 (ttp-170) REVERT: C 34 LEU cc_start: 0.8612 (mt) cc_final: 0.8361 (mt) REVERT: C 58 LEU cc_start: 0.9538 (mt) cc_final: 0.9326 (mt) REVERT: C 71 ARG cc_start: 0.8359 (ttm110) cc_final: 0.7865 (ttp-110) REVERT: C 75 LYS cc_start: 0.9136 (mmtm) cc_final: 0.8822 (mmmm) REVERT: C 89 ASN cc_start: 0.8558 (m-40) cc_final: 0.8153 (m110) REVERT: C 110 ASN cc_start: 0.9193 (t0) cc_final: 0.8971 (t0) REVERT: D 31 LYS cc_start: 0.8602 (mppt) cc_final: 0.8195 (mmtm) REVERT: D 64 ASN cc_start: 0.8723 (m-40) cc_final: 0.8123 (m-40) REVERT: D 73 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8678 (mm-30) REVERT: D 76 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7916 (ttp-110) REVERT: D 92 GLN cc_start: 0.8399 (pt0) cc_final: 0.7608 (pp30) REVERT: D 102 GLU cc_start: 0.7888 (tp30) cc_final: 0.7644 (tp30) REVERT: D 105 LYS cc_start: 0.8303 (tptp) cc_final: 0.7735 (tptp) REVERT: D 109 SER cc_start: 0.9372 (t) cc_final: 0.8624 (p) REVERT: D 113 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8865 (mmtm) REVERT: F 63 GLU cc_start: 0.7632 (pp20) cc_final: 0.7174 (pp20) REVERT: F 70 VAL cc_start: 0.9110 (t) cc_final: 0.8856 (p) REVERT: F 79 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8635 (mmtm) REVERT: F 88 TYR cc_start: 0.9295 (m-10) cc_final: 0.8803 (m-80) REVERT: F 90 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9100 (mp) REVERT: F 95 ARG cc_start: 0.8471 (mpp80) cc_final: 0.8130 (mtt90) REVERT: G 17 ARG cc_start: 0.8729 (ptp-170) cc_final: 0.8155 (ptp-110) REVERT: G 18 SER cc_start: 0.9138 (m) cc_final: 0.8860 (t) REVERT: G 20 ARG cc_start: 0.8587 (mtt90) cc_final: 0.7088 (mtt-85) REVERT: G 29 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7149 (tpp80) REVERT: G 42 ARG cc_start: 0.8717 (mtm180) cc_final: 0.8098 (mtm180) REVERT: G 61 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8342 (mm-30) REVERT: G 79 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8435 (mm) REVERT: G 81 ARG cc_start: 0.9112 (tpt90) cc_final: 0.8596 (tpt90) REVERT: G 112 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8270 (mm-40) REVERT: H 33 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8140 (t) REVERT: H 48 ASP cc_start: 0.8449 (m-30) cc_final: 0.8197 (p0) REVERT: H 73 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8665 (mm-30) REVERT: H 76 ARG cc_start: 0.9177 (mtm110) cc_final: 0.8920 (mtm110) REVERT: H 89 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7461 (ptm-80) REVERT: H 117 LYS cc_start: 0.9154 (tppt) cc_final: 0.8699 (tptp) REVERT: A 63 ARG cc_start: 0.8515 (mmp80) cc_final: 0.7818 (mmp80) REVERT: A 76 GLN cc_start: 0.8811 (mm110) cc_final: 0.8532 (mm-40) REVERT: E 39 HIS cc_start: 0.7632 (p-80) cc_final: 0.7351 (p-80) REVERT: E 53 ARG cc_start: 0.8500 (tpt90) cc_final: 0.8264 (tpt90) REVERT: E 56 LYS cc_start: 0.8584 (mmtm) cc_final: 0.8095 (mmtm) REVERT: E 60 LEU cc_start: 0.9145 (mm) cc_final: 0.8873 (mm) REVERT: E 65 LEU cc_start: 0.8871 (tt) cc_final: 0.8097 (tt) REVERT: E 68 GLN cc_start: 0.8420 (pp30) cc_final: 0.7992 (pp30) REVERT: E 73 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8151 (tp30) REVERT: E 76 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8717 (tm-30) REVERT: E 83 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.7288 (tpm170) REVERT: E 87 SER cc_start: 0.9185 (m) cc_final: 0.8934 (p) REVERT: E 93 GLN cc_start: 0.8122 (tm-30) cc_final: 0.6467 (tm-30) REVERT: E 94 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8298 (mt-10) REVERT: E 97 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7786 (mt-10) REVERT: E 105 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7598 (tm-30) REVERT: E 117 VAL cc_start: 0.9437 (t) cc_final: 0.9223 (p) outliers start: 34 outliers final: 22 residues processed: 400 average time/residue: 0.1677 time to fit residues: 86.9285 Evaluate side-chains 403 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 376 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.137669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094783 restraints weight = 30596.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097766 restraints weight = 17242.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099668 restraints weight = 12055.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.100783 restraints weight = 9684.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.101611 restraints weight = 8523.292| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13814 Z= 0.196 Angle : 0.688 14.559 19943 Z= 0.383 Chirality : 0.036 0.203 2253 Planarity : 0.005 0.059 1485 Dihedral : 29.657 149.156 4233 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.89 % Allowed : 36.33 % Favored : 57.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.28), residues: 831 helix: 1.02 (0.22), residues: 532 sheet: -3.52 (1.40), residues: 10 loop : -0.60 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 35 TYR 0.034 0.002 TYR D 80 PHE 0.020 0.002 PHE B 61 TRP 0.001 0.000 TRP K 82 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00450 (13814) covalent geometry : angle 0.68823 (19943) hydrogen bonds : bond 0.05142 ( 658) hydrogen bonds : angle 3.28866 ( 1637) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 384 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.9453 (ttmm) cc_final: 0.8947 (tptp) REVERT: B 39 ARG cc_start: 0.9158 (mmt90) cc_final: 0.8568 (tpp-160) REVERT: B 44 LYS cc_start: 0.9326 (tttt) cc_final: 0.8944 (mttp) REVERT: B 45 ARG cc_start: 0.9005 (mtp-110) cc_final: 0.8751 (mtp85) REVERT: B 55 ARG cc_start: 0.8675 (mtt90) cc_final: 0.8353 (ttm110) REVERT: B 63 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7710 (mt-10) REVERT: B 79 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8768 (mmmm) REVERT: C 20 ARG cc_start: 0.8848 (mmt-90) cc_final: 0.8518 (mpt-90) REVERT: C 24 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8468 (mm110) REVERT: C 29 ARG cc_start: 0.8006 (tpp80) cc_final: 0.7106 (tpp80) REVERT: C 34 LEU cc_start: 0.8648 (mt) cc_final: 0.8351 (mt) REVERT: C 56 GLU cc_start: 0.8591 (tt0) cc_final: 0.8367 (mt-10) REVERT: C 75 LYS cc_start: 0.9099 (mmtm) cc_final: 0.8809 (mmmm) REVERT: C 108 LEU cc_start: 0.8688 (mt) cc_final: 0.8144 (tt) REVERT: D 31 LYS cc_start: 0.8644 (mppt) cc_final: 0.8223 (mmtm) REVERT: D 43 LYS cc_start: 0.9216 (mmmt) cc_final: 0.8988 (tppt) REVERT: D 64 ASN cc_start: 0.8869 (m-40) cc_final: 0.8472 (m110) REVERT: D 73 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8717 (mm-30) REVERT: D 92 GLN cc_start: 0.8404 (pt0) cc_final: 0.7628 (pp30) REVERT: D 102 GLU cc_start: 0.8008 (tp30) cc_final: 0.7584 (tp30) REVERT: D 105 LYS cc_start: 0.8370 (tptp) cc_final: 0.7752 (tptp) REVERT: D 109 SER cc_start: 0.9360 (t) cc_final: 0.8434 (p) REVERT: D 110 GLU cc_start: 0.9062 (tt0) cc_final: 0.8761 (tt0) REVERT: F 31 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8617 (tppp) REVERT: F 70 VAL cc_start: 0.9110 (t) cc_final: 0.8868 (p) REVERT: F 88 TYR cc_start: 0.9343 (m-10) cc_final: 0.8780 (m-80) REVERT: F 90 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9130 (mp) REVERT: F 95 ARG cc_start: 0.8489 (mpp80) cc_final: 0.8288 (mtt90) REVERT: G 17 ARG cc_start: 0.8813 (ptp-170) cc_final: 0.8141 (ptp-110) REVERT: G 18 SER cc_start: 0.9275 (m) cc_final: 0.9070 (t) REVERT: G 29 ARG cc_start: 0.7875 (tpp80) cc_final: 0.6913 (tpp80) REVERT: G 35 ARG cc_start: 0.8091 (tpp-160) cc_final: 0.7491 (mmm160) REVERT: G 42 ARG cc_start: 0.8678 (mtm180) cc_final: 0.8075 (mtm180) REVERT: G 61 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8201 (mm-30) REVERT: G 81 ARG cc_start: 0.8987 (tpt90) cc_final: 0.8577 (tpt90) REVERT: G 85 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9115 (mt) REVERT: G 89 ASN cc_start: 0.8726 (m-40) cc_final: 0.8518 (m110) REVERT: G 95 LYS cc_start: 0.9010 (pttm) cc_final: 0.8776 (pttm) REVERT: H 40 LYS cc_start: 0.9226 (tptt) cc_final: 0.8819 (tptt) REVERT: H 43 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.7968 (ptpp) REVERT: H 48 ASP cc_start: 0.8452 (m-30) cc_final: 0.8251 (p0) REVERT: H 73 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8441 (mm-30) REVERT: H 89 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7226 (ptm-80) REVERT: H 117 LYS cc_start: 0.9258 (tppt) cc_final: 0.8716 (tptp) REVERT: A 49 ARG cc_start: 0.8786 (mtp-110) cc_final: 0.8386 (mtp85) REVERT: A 63 ARG cc_start: 0.8410 (mmp80) cc_final: 0.8201 (mmp80) REVERT: A 76 GLN cc_start: 0.8848 (mm110) cc_final: 0.8599 (mm-40) REVERT: A 79 LYS cc_start: 0.9221 (tptp) cc_final: 0.8940 (tptp) REVERT: E 53 ARG cc_start: 0.8595 (tpt90) cc_final: 0.7951 (tpt90) REVERT: E 60 LEU cc_start: 0.9144 (mm) cc_final: 0.8842 (mm) REVERT: E 65 LEU cc_start: 0.8985 (tt) cc_final: 0.8212 (tt) REVERT: E 68 GLN cc_start: 0.8442 (pp30) cc_final: 0.7958 (pp30) REVERT: E 76 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8885 (tm-30) REVERT: E 83 ARG cc_start: 0.7639 (tpp-160) cc_final: 0.7272 (tpp80) REVERT: E 87 SER cc_start: 0.9253 (m) cc_final: 0.9012 (p) REVERT: E 93 GLN cc_start: 0.8074 (tm-30) cc_final: 0.6800 (tm-30) REVERT: E 94 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8160 (mt-10) REVERT: E 97 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7788 (mt-10) REVERT: E 105 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 115 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8478 (mmmm) REVERT: E 117 VAL cc_start: 0.9493 (t) cc_final: 0.9288 (p) outliers start: 42 outliers final: 31 residues processed: 400 average time/residue: 0.1629 time to fit residues: 85.0162 Evaluate side-chains 410 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 375 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 10.0000 chunk 87 optimal weight: 0.0970 chunk 97 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 89 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.139668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097048 restraints weight = 30676.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100127 restraints weight = 17078.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.102115 restraints weight = 11827.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.103374 restraints weight = 9425.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104138 restraints weight = 8197.198| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.7464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13814 Z= 0.171 Angle : 0.705 16.226 19943 Z= 0.389 Chirality : 0.036 0.208 2253 Planarity : 0.005 0.061 1485 Dihedral : 29.614 148.760 4233 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.21 % Allowed : 40.25 % Favored : 55.54 % 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 are not related in a simple way. whole: 0.49 (0.28), residues: 831 helix: 0.96 (0.22), residues: 528 sheet: -3.53 (1.36), residues: 10 loop : -0.59 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 92 TYR 0.049 0.002 TYR D 80 PHE 0.025 0.002 PHE B 61 TRP 0.001 0.000 TRP K 82 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00390 (13814) covalent geometry : angle 0.70543 (19943) hydrogen bonds : bond 0.04934 ( 658) hydrogen bonds : angle 3.24564 ( 1637) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 379 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.9432 (ttmm) cc_final: 0.9226 (tppt) REVERT: B 73 THR cc_start: 0.9208 (t) cc_final: 0.8992 (t) REVERT: B 79 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8726 (mmmm) REVERT: C 17 ARG cc_start: 0.8925 (mtm180) cc_final: 0.8577 (mtt90) REVERT: C 20 ARG cc_start: 0.8796 (mmt-90) cc_final: 0.8412 (mpt-90) REVERT: C 24 GLN cc_start: 0.9063 (mm-40) cc_final: 0.7973 (mm-40) REVERT: C 25 PHE cc_start: 0.8876 (m-10) cc_final: 0.8348 (m-10) REVERT: C 29 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7062 (tpp80) REVERT: C 34 LEU cc_start: 0.8580 (mt) cc_final: 0.8260 (mt) REVERT: C 35 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7858 (tpm170) REVERT: C 56 GLU cc_start: 0.8582 (tt0) cc_final: 0.8206 (mm-30) REVERT: C 75 LYS cc_start: 0.9029 (mmtm) cc_final: 0.8820 (mmmm) REVERT: D 31 LYS cc_start: 0.8725 (mppt) cc_final: 0.8296 (mmtm) REVERT: D 39 TYR cc_start: 0.8140 (t80) cc_final: 0.7423 (t80) REVERT: D 43 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8966 (tppt) REVERT: D 64 ASN cc_start: 0.8832 (m-40) cc_final: 0.8370 (m110) REVERT: D 73 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8270 (mm-30) REVERT: D 92 GLN cc_start: 0.8369 (pt0) cc_final: 0.7596 (pp30) REVERT: D 102 GLU cc_start: 0.7941 (tp30) cc_final: 0.7565 (tp30) REVERT: D 105 LYS cc_start: 0.8445 (tptp) cc_final: 0.7855 (tptp) REVERT: D 109 SER cc_start: 0.9180 (t) cc_final: 0.8696 (p) REVERT: D 110 GLU cc_start: 0.9005 (tt0) cc_final: 0.8684 (tt0) REVERT: D 113 LYS cc_start: 0.9140 (mtmm) cc_final: 0.8697 (mptt) REVERT: F 31 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8228 (tppp) REVERT: F 51 TYR cc_start: 0.8230 (m-10) cc_final: 0.7780 (m-10) REVERT: F 70 VAL cc_start: 0.9109 (t) cc_final: 0.8883 (p) REVERT: F 88 TYR cc_start: 0.9266 (m-10) cc_final: 0.8729 (m-80) REVERT: F 90 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9094 (mp) REVERT: F 95 ARG cc_start: 0.8418 (mpp80) cc_final: 0.8132 (mtt90) REVERT: G 17 ARG cc_start: 0.8866 (ptp-170) cc_final: 0.8179 (ptp-110) REVERT: G 18 SER cc_start: 0.9264 (m) cc_final: 0.9038 (t) REVERT: G 29 ARG cc_start: 0.7789 (tpp80) cc_final: 0.6861 (tpp80) REVERT: G 35 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7506 (mmm160) REVERT: G 38 ASN cc_start: 0.8787 (m-40) cc_final: 0.7631 (t0) REVERT: G 42 ARG cc_start: 0.8584 (mtm180) cc_final: 0.8032 (mtm180) REVERT: G 61 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8338 (mm-30) REVERT: G 81 ARG cc_start: 0.9083 (tpt90) cc_final: 0.8593 (tpt90) REVERT: H 30 ARG cc_start: 0.7587 (ptm-80) cc_final: 0.7381 (ptm-80) REVERT: H 73 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8429 (mm-30) REVERT: H 76 ARG cc_start: 0.9151 (mtm110) cc_final: 0.8490 (mtm110) REVERT: H 89 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7534 (ptm-80) REVERT: H 117 LYS cc_start: 0.9276 (tppt) cc_final: 0.8815 (tptp) REVERT: H 120 SER cc_start: 0.9547 (m) cc_final: 0.9244 (p) REVERT: A 49 ARG cc_start: 0.8838 (mtp-110) cc_final: 0.8306 (ttt180) REVERT: A 76 GLN cc_start: 0.8803 (mm110) cc_final: 0.8570 (mm-40) REVERT: A 79 LYS cc_start: 0.9185 (tptp) cc_final: 0.8936 (tptp) REVERT: E 56 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8302 (mmtm) REVERT: E 60 LEU cc_start: 0.9146 (mm) cc_final: 0.8825 (mm) REVERT: E 65 LEU cc_start: 0.8975 (tt) cc_final: 0.8131 (tt) REVERT: E 76 GLN cc_start: 0.9346 (tm-30) cc_final: 0.8896 (tm-30) REVERT: E 87 SER cc_start: 0.9188 (m) cc_final: 0.8910 (p) REVERT: E 93 GLN cc_start: 0.7920 (tm-30) cc_final: 0.6690 (tm-30) REVERT: E 94 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8149 (mt-10) REVERT: E 105 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7650 (tm-30) REVERT: E 117 VAL cc_start: 0.9548 (t) cc_final: 0.9298 (p) outliers start: 30 outliers final: 24 residues processed: 390 average time/residue: 0.1583 time to fit residues: 80.5979 Evaluate side-chains 394 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 368 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 0.0030 chunk 46 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.0154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 85 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.137309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.094964 restraints weight = 31111.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098031 restraints weight = 17297.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100059 restraints weight = 11952.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101365 restraints weight = 9466.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102144 restraints weight = 8205.134| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.7695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13814 Z= 0.210 Angle : 0.751 16.486 19943 Z= 0.412 Chirality : 0.038 0.207 2253 Planarity : 0.006 0.059 1485 Dihedral : 29.662 148.261 4233 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.35 % Allowed : 39.97 % Favored : 55.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.28), residues: 831 helix: 0.79 (0.22), residues: 529 sheet: -3.41 (1.34), residues: 10 loop : -0.56 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 53 TYR 0.100 0.003 TYR B 88 PHE 0.022 0.002 PHE B 61 TRP 0.001 0.000 TRP K 82 HIS 0.004 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00484 (13814) covalent geometry : angle 0.75133 (19943) hydrogen bonds : bond 0.05224 ( 658) hydrogen bonds : angle 3.42064 ( 1637) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 372 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7706 (mt-10) REVERT: B 79 LYS cc_start: 0.9262 (mmmm) cc_final: 0.8893 (mmmm) REVERT: C 20 ARG cc_start: 0.8836 (mmt-90) cc_final: 0.8467 (mpt-90) REVERT: C 24 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8014 (mm110) REVERT: C 29 ARG cc_start: 0.7994 (tpp80) cc_final: 0.7093 (tpp80) REVERT: C 35 ARG cc_start: 0.8290 (tpp80) cc_final: 0.7667 (mmp-170) REVERT: C 56 GLU cc_start: 0.8588 (tt0) cc_final: 0.8299 (mm-30) REVERT: C 75 LYS cc_start: 0.9128 (mmtm) cc_final: 0.8916 (mmmm) REVERT: D 31 LYS cc_start: 0.8696 (mppt) cc_final: 0.8247 (mmtm) REVERT: D 39 TYR cc_start: 0.8320 (t80) cc_final: 0.7707 (t80) REVERT: D 41 VAL cc_start: 0.9214 (t) cc_final: 0.8715 (p) REVERT: D 43 LYS cc_start: 0.9230 (mmmt) cc_final: 0.8975 (tppt) REVERT: D 64 ASN cc_start: 0.8813 (m-40) cc_final: 0.8354 (m-40) REVERT: D 73 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7570 (mm-30) REVERT: D 76 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.6678 (ttt-90) REVERT: D 92 GLN cc_start: 0.8298 (pt0) cc_final: 0.7624 (pp30) REVERT: D 102 GLU cc_start: 0.8048 (tp30) cc_final: 0.7643 (tp30) REVERT: D 105 LYS cc_start: 0.8511 (tptp) cc_final: 0.7953 (tptp) REVERT: D 109 SER cc_start: 0.9423 (t) cc_final: 0.8727 (p) REVERT: D 110 GLU cc_start: 0.8989 (tt0) cc_final: 0.8746 (tp30) REVERT: D 113 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8745 (mppt) REVERT: F 31 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8269 (tppp) REVERT: F 51 TYR cc_start: 0.8330 (m-10) cc_final: 0.7875 (m-10) REVERT: F 70 VAL cc_start: 0.9123 (t) cc_final: 0.8901 (p) REVERT: F 80 THR cc_start: 0.8850 (p) cc_final: 0.8614 (p) REVERT: F 88 TYR cc_start: 0.9350 (m-10) cc_final: 0.8771 (m-80) REVERT: F 90 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9148 (mp) REVERT: F 92 ARG cc_start: 0.8865 (mmm160) cc_final: 0.8518 (mmm-85) REVERT: F 95 ARG cc_start: 0.8558 (mpp80) cc_final: 0.8348 (mtt90) REVERT: G 17 ARG cc_start: 0.8785 (ptp-170) cc_final: 0.8163 (ptp-110) REVERT: G 29 ARG cc_start: 0.7814 (tpp80) cc_final: 0.6863 (tpp80) REVERT: G 35 ARG cc_start: 0.7986 (tpp-160) cc_final: 0.7479 (mmm160) REVERT: G 38 ASN cc_start: 0.8851 (m-40) cc_final: 0.7689 (t0) REVERT: G 42 ARG cc_start: 0.8712 (mtm180) cc_final: 0.8141 (mtm180) REVERT: G 61 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8221 (mm-30) REVERT: G 81 ARG cc_start: 0.8950 (tpt90) cc_final: 0.8572 (tpt90) REVERT: G 89 ASN cc_start: 0.8493 (m-40) cc_final: 0.8253 (m110) REVERT: G 90 ASP cc_start: 0.8284 (t70) cc_final: 0.7986 (t70) REVERT: H 30 ARG cc_start: 0.7531 (ptm-80) cc_final: 0.7323 (ptm-80) REVERT: H 89 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7692 (ptm-80) REVERT: H 113 LYS cc_start: 0.9180 (tptt) cc_final: 0.8739 (tppt) REVERT: H 117 LYS cc_start: 0.9316 (tppt) cc_final: 0.8863 (tptp) REVERT: H 120 SER cc_start: 0.9519 (m) cc_final: 0.9237 (p) REVERT: A 42 ARG cc_start: 0.7699 (mmm-85) cc_final: 0.7367 (mmm160) REVERT: A 49 ARG cc_start: 0.8877 (mtp-110) cc_final: 0.8340 (ttt180) REVERT: A 76 GLN cc_start: 0.8854 (mm110) cc_final: 0.8626 (mm-40) REVERT: A 79 LYS cc_start: 0.9212 (tptp) cc_final: 0.8976 (tptp) REVERT: E 53 ARG cc_start: 0.8564 (tpt90) cc_final: 0.8084 (tmt-80) REVERT: E 54 TYR cc_start: 0.8237 (m-10) cc_final: 0.7685 (m-10) REVERT: E 56 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8353 (mmtm) REVERT: E 60 LEU cc_start: 0.9134 (mm) cc_final: 0.8828 (mm) REVERT: E 63 ARG cc_start: 0.7778 (mmp80) cc_final: 0.7270 (mmp80) REVERT: E 73 GLU cc_start: 0.8380 (tp30) cc_final: 0.8108 (tp30) REVERT: E 76 GLN cc_start: 0.9314 (tm-30) cc_final: 0.8904 (tm-30) REVERT: E 83 ARG cc_start: 0.7799 (tpp-160) cc_final: 0.7480 (tpp80) REVERT: E 87 SER cc_start: 0.9195 (m) cc_final: 0.8990 (p) REVERT: E 93 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7454 (tm-30) REVERT: E 94 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8189 (mt-10) REVERT: E 105 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7603 (tm-30) REVERT: E 115 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8489 (mmmm) outliers start: 31 outliers final: 26 residues processed: 383 average time/residue: 0.1638 time to fit residues: 81.7170 Evaluate side-chains 397 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 369 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.0000 chunk 16 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.139422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.097744 restraints weight = 30598.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.100874 restraints weight = 16860.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102928 restraints weight = 11609.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104224 restraints weight = 9153.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.104962 restraints weight = 7920.134| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.7908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13814 Z= 0.175 Angle : 0.738 16.213 19943 Z= 0.403 Chirality : 0.037 0.211 2253 Planarity : 0.005 0.061 1485 Dihedral : 29.657 147.853 4233 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.79 % Allowed : 42.08 % Favored : 54.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.28), residues: 831 helix: 0.79 (0.22), residues: 531 sheet: -3.53 (1.23), residues: 10 loop : -0.54 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 76 TYR 0.068 0.002 TYR B 88 PHE 0.022 0.001 PHE B 61 TRP 0.001 0.000 TRP K 82 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00400 (13814) covalent geometry : angle 0.73800 (19943) hydrogen bonds : bond 0.04913 ( 658) hydrogen bonds : angle 3.36349 ( 1637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.09 seconds wall clock time: 47 minutes 44.66 seconds (2864.66 seconds total)