Starting phenix.real_space_refine on Wed Jul 30 18:06:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbq_16549/07_2025/8cbq_16549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbq_16549/07_2025/8cbq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cbq_16549/07_2025/8cbq_16549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbq_16549/07_2025/8cbq_16549.map" model { file = "/net/cci-nas-00/data/ceres_data/8cbq_16549/07_2025/8cbq_16549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbq_16549/07_2025/8cbq_16549.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.38, per 1000 atoms: 0.57 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: 2.81 Conformation dependent library (CDL) restraints added in 935.2 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: 6.31 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: 4.45 Time building geometry restraints manager: 3.42 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.120 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.002 TRP K 82 HIS 0.004 0.001 HIS K 20 PHE 0.013 0.002 PHE G 25 TYR 0.012 0.002 TYR B 72 ARG 0.004 0.001 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.31386 ( 658) hydrogen bonds : angle 10.64236 ( 1637) covalent geometry : bond 0.00834 (13814) covalent geometry : angle 0.72447 (19943) *********************** 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 : 0.921 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: 0.7238 (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: 0.3672 time to fit residues: 219.7882 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 : 0.924 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.5980 chunk 84 optimal weight: 30.0000 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.0570 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.148329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.105769 restraints weight = 29163.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109298 restraints weight = 15388.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.111551 restraints weight = 10329.184| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 13814 Z= 0.186 Angle : 0.702 7.390 19943 Z= 0.403 Chirality : 0.038 0.207 2253 Planarity : 0.007 0.072 1485 Dihedral : 29.778 157.635 4250 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.91 % Allowed : 22.30 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.24), residues: 831 helix: -1.79 (0.18), residues: 526 sheet: -4.30 (1.24), residues: 10 loop : -1.42 (0.30), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.007 0.001 HIS E 113 PHE 0.020 0.002 PHE H 62 TYR 0.020 0.002 TYR F 51 ARG 0.017 0.001 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.06422 ( 658) hydrogen bonds : angle 3.52537 ( 1637) covalent geometry : bond 0.00418 (13814) covalent geometry : angle 0.70219 (19943) *********************** 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: 35 poor density : 402 time to evaluate : 0.909 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: B 25 ASN cc_start: 0.9033 (m110) cc_final: 0.8752 (m110) REVERT: B 79 LYS cc_start: 0.8875 (mmtp) cc_final: 0.8419 (mmtm) REVERT: C 32 ARG cc_start: 0.7912 (ttp80) cc_final: 0.6993 (ttp80) REVERT: C 71 ARG cc_start: 0.7418 (ttm110) cc_final: 0.6937 (ttp-110) REVERT: C 75 LYS cc_start: 0.8402 (mmmm) cc_final: 0.7957 (mmmm) REVERT: C 110 ASN cc_start: 0.8903 (t0) cc_final: 0.8401 (t0) REVERT: C 115 LEU cc_start: 0.9268 (mt) cc_final: 0.9003 (mp) REVERT: D 34 TYR cc_start: 0.8601 (m-80) cc_final: 0.8387 (m-10) REVERT: D 49 THR cc_start: 0.8477 (m) cc_final: 0.8120 (p) REVERT: D 59 MET cc_start: 0.9700 (mmm) cc_final: 0.9103 (tpp) REVERT: D 64 ASN cc_start: 0.8804 (m110) cc_final: 0.8208 (m110) REVERT: D 65 ASP cc_start: 0.8776 (t70) cc_final: 0.8362 (t70) REVERT: D 105 LYS cc_start: 0.8659 (tptp) cc_final: 0.8410 (tptp) REVERT: D 110 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7689 (mt-10) REVERT: D 113 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8804 (mmtm) REVERT: F 25 ASN cc_start: 0.8616 (m-40) cc_final: 0.8086 (m-40) REVERT: F 39 ARG cc_start: 0.9173 (mmt-90) cc_final: 0.8753 (mmt180) REVERT: F 53 GLU cc_start: 0.8507 (tp30) cc_final: 0.7748 (tp30) REVERT: F 75 HIS cc_start: 0.8286 (t70) cc_final: 0.7869 (t70) REVERT: F 79 LYS cc_start: 0.9000 (mmtm) cc_final: 0.8759 (mmtm) REVERT: F 88 TYR cc_start: 0.9273 (m-10) cc_final: 0.8757 (m-80) REVERT: F 92 ARG cc_start: 0.8946 (mmm160) cc_final: 0.8737 (mmm-85) REVERT: G 17 ARG cc_start: 0.8154 (mtm180) cc_final: 0.7705 (ptp-170) REVERT: G 42 ARG cc_start: 0.8660 (mtp-110) cc_final: 0.8195 (mtm-85) REVERT: G 61 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8015 (mm-30) REVERT: G 73 ASN cc_start: 0.8755 (t0) cc_final: 0.8279 (t0) REVERT: G 81 ARG cc_start: 0.8539 (tpt90) cc_final: 0.8260 (tpt90) REVERT: G 101 THR cc_start: 0.9191 (m) cc_final: 0.8944 (p) REVERT: G 110 ASN cc_start: 0.8940 (t0) cc_final: 0.8378 (t0) REVERT: G 112 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8320 (mm110) REVERT: H 34 TYR cc_start: 0.8033 (m-80) cc_final: 0.7458 (m-10) REVERT: H 39 TYR cc_start: 0.8257 (t80) cc_final: 0.7926 (t80) REVERT: H 40 LYS cc_start: 0.8859 (tppt) cc_final: 0.8429 (tppt) REVERT: H 43 LYS cc_start: 0.8536 (pptt) cc_final: 0.7920 (pptt) REVERT: H 44 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8238 (mm-40) REVERT: H 102 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8362 (mm-30) REVERT: K 40 LEU cc_start: 0.4481 (OUTLIER) cc_final: 0.4031 (tp) REVERT: A 40 ARG cc_start: 0.8325 (mtm110) cc_final: 0.8106 (mtp180) REVERT: A 55 GLN cc_start: 0.9262 (mt0) cc_final: 0.8768 (tt0) REVERT: A 56 LYS cc_start: 0.8472 (pttp) cc_final: 0.8087 (pttt) REVERT: A 76 GLN cc_start: 0.8736 (mm110) cc_final: 0.8191 (mm-40) REVERT: A 79 LYS cc_start: 0.8792 (tptp) cc_final: 0.8542 (tptt) REVERT: A 106 ASP cc_start: 0.8778 (m-30) cc_final: 0.8440 (m-30) REVERT: A 129 ARG cc_start: 0.8843 (mmm-85) cc_final: 0.8132 (mmp80) REVERT: E 41 TYR cc_start: 0.8144 (m-80) cc_final: 0.7559 (m-80) REVERT: E 49 ARG cc_start: 0.8479 (ptm160) cc_final: 0.8034 (ptp-170) REVERT: E 50 GLU cc_start: 0.8336 (pt0) cc_final: 0.7952 (pt0) REVERT: E 68 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7743 (pp30) REVERT: E 71 VAL cc_start: 0.9120 (t) cc_final: 0.8857 (t) REVERT: E 85 GLN cc_start: 0.7892 (mt0) cc_final: 0.7520 (mt0) REVERT: E 105 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7483 (tm-30) REVERT: E 113 HIS cc_start: 0.7682 (t70) cc_final: 0.7349 (t70) REVERT: E 117 VAL cc_start: 0.9167 (t) cc_final: 0.8874 (p) REVERT: E 119 ILE cc_start: 0.9043 (pt) cc_final: 0.8126 (pt) REVERT: E 120 MET cc_start: 0.6764 (mtt) cc_final: 0.6393 (mpp) REVERT: E 125 GLN cc_start: 0.8726 (mt0) cc_final: 0.8372 (mm-40) outliers start: 35 outliers final: 22 residues processed: 417 average time/residue: 0.3441 time to fit residues: 186.6872 Evaluate side-chains 389 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 366 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 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 53 SER 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 84 SER 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 89 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 4 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 D 46 HIS F 75 HIS G 89 ASN H 92 GLN H 106 HIS ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 108 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.140168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095564 restraints weight = 29387.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098707 restraints weight = 16201.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.100752 restraints weight = 11214.401| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5076 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= 0.217 Angle : 0.697 12.401 19943 Z= 0.395 Chirality : 0.037 0.196 2253 Planarity : 0.006 0.062 1485 Dihedral : 29.639 152.184 4242 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 6.73 % Allowed : 26.93 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.27), residues: 831 helix: -0.06 (0.22), residues: 535 sheet: -4.15 (1.19), residues: 10 loop : -1.19 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 82 HIS 0.006 0.001 HIS E 113 PHE 0.015 0.002 PHE A 84 TYR 0.019 0.002 TYR F 51 ARG 0.018 0.001 ARG G 17 Details of bonding type rmsd hydrogen bonds : bond 0.06042 ( 658) hydrogen bonds : angle 3.38895 ( 1637) covalent geometry : bond 0.00488 (13814) covalent geometry : angle 0.69732 (19943) *********************** 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 443 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 395 time to evaluate : 0.904 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 25 ASN cc_start: 0.9082 (m110) cc_final: 0.8694 (m-40) REVERT: B 45 ARG cc_start: 0.9062 (mtp-110) cc_final: 0.8762 (ttp80) REVERT: B 63 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 79 LYS cc_start: 0.9092 (mmtp) cc_final: 0.8792 (mmmm) REVERT: C 17 ARG cc_start: 0.8921 (mtm180) cc_final: 0.8448 (mtp180) REVERT: C 32 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7504 (ttt180) REVERT: C 71 ARG cc_start: 0.7946 (ttm110) cc_final: 0.7554 (ttp-110) REVERT: C 89 ASN cc_start: 0.8643 (m110) cc_final: 0.8362 (m-40) REVERT: C 95 LYS cc_start: 0.9178 (pttt) cc_final: 0.8849 (ptpp) REVERT: C 110 ASN cc_start: 0.9047 (t0) cc_final: 0.8661 (t0) REVERT: C 115 LEU cc_start: 0.9012 (mt) cc_final: 0.8714 (mm) REVERT: C 116 LEU cc_start: 0.8955 (tp) cc_final: 0.8713 (mt) REVERT: D 49 THR cc_start: 0.8552 (m) cc_final: 0.8209 (p) REVERT: D 59 MET cc_start: 0.9687 (mmm) cc_final: 0.9427 (tpp) REVERT: D 64 ASN cc_start: 0.8849 (m110) cc_final: 0.8476 (m110) REVERT: D 65 ASP cc_start: 0.8760 (t70) cc_final: 0.8549 (t70) REVERT: D 73 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8911 (mm-30) REVERT: D 83 ARG cc_start: 0.8125 (mmt90) cc_final: 0.7918 (mmt90) REVERT: D 92 GLN cc_start: 0.8262 (pt0) cc_final: 0.7923 (pp30) REVERT: D 102 GLU cc_start: 0.8029 (tp30) cc_final: 0.7635 (tp30) REVERT: D 105 LYS cc_start: 0.8810 (tptp) cc_final: 0.8308 (tptp) REVERT: D 109 SER cc_start: 0.9441 (t) cc_final: 0.8877 (p) REVERT: D 110 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7945 (mt-10) REVERT: D 113 LYS cc_start: 0.9004 (mmtm) cc_final: 0.8781 (mmtm) REVERT: D 117 LYS cc_start: 0.9346 (ttpt) cc_final: 0.9105 (pttp) REVERT: F 25 ASN cc_start: 0.8724 (m-40) cc_final: 0.8497 (m-40) REVERT: F 44 LYS cc_start: 0.9013 (mtmm) cc_final: 0.8453 (mtmm) REVERT: F 45 ARG cc_start: 0.9155 (mtp180) cc_final: 0.8004 (mmm-85) REVERT: F 53 GLU cc_start: 0.8560 (tp30) cc_final: 0.8038 (tp30) REVERT: F 63 GLU cc_start: 0.8129 (pt0) cc_final: 0.7781 (pp20) REVERT: F 74 GLU cc_start: 0.8559 (tp30) cc_final: 0.8344 (tp30) REVERT: F 88 TYR cc_start: 0.9380 (m-10) cc_final: 0.8857 (m-80) REVERT: G 39 TYR cc_start: 0.9124 (m-80) cc_final: 0.8553 (m-80) REVERT: G 42 ARG cc_start: 0.8458 (mtp-110) cc_final: 0.8061 (mtm-85) REVERT: G 58 LEU cc_start: 0.8563 (mt) cc_final: 0.8234 (mp) REVERT: G 61 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8281 (mm-30) REVERT: G 64 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7640 (tm-30) REVERT: G 68 ASN cc_start: 0.8472 (p0) cc_final: 0.7981 (p0) REVERT: G 72 ASP cc_start: 0.7839 (m-30) cc_final: 0.7589 (m-30) REVERT: G 78 ILE cc_start: 0.8770 (mt) cc_final: 0.8439 (mt) REVERT: G 81 ARG cc_start: 0.8798 (tpt90) cc_final: 0.8585 (tpt90) REVERT: G 95 LYS cc_start: 0.9153 (pttp) cc_final: 0.8793 (pttm) REVERT: H 40 LYS cc_start: 0.9498 (tppt) cc_final: 0.9028 (tppt) REVERT: H 44 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8531 (mm110) REVERT: H 56 MET cc_start: 0.8091 (tmm) cc_final: 0.7866 (tmm) REVERT: H 59 MET cc_start: 0.9238 (mmp) cc_final: 0.9015 (mmp) REVERT: H 102 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8055 (mm-30) REVERT: H 105 LYS cc_start: 0.9238 (ptmm) cc_final: 0.8712 (pttm) REVERT: K 40 LEU cc_start: 0.4771 (OUTLIER) cc_final: 0.4448 (tp) REVERT: A 74 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9178 (tp) REVERT: A 76 GLN cc_start: 0.8694 (mm110) cc_final: 0.8435 (mm-40) REVERT: A 79 LYS cc_start: 0.9121 (tptp) cc_final: 0.8753 (tptt) REVERT: A 83 ARG cc_start: 0.8103 (mmp80) cc_final: 0.7857 (mmp80) REVERT: E 39 HIS cc_start: 0.7340 (p-80) cc_final: 0.6887 (p-80) REVERT: E 41 TYR cc_start: 0.8298 (m-80) cc_final: 0.8063 (m-80) REVERT: E 49 ARG cc_start: 0.8647 (ptm160) cc_final: 0.7987 (ptp90) REVERT: E 50 GLU cc_start: 0.8272 (pt0) cc_final: 0.7716 (pt0) REVERT: E 57 SER cc_start: 0.8697 (p) cc_final: 0.8321 (p) REVERT: E 63 ARG cc_start: 0.7884 (mmp80) cc_final: 0.7657 (mmp80) REVERT: E 67 PHE cc_start: 0.8947 (t80) cc_final: 0.8101 (t80) REVERT: E 68 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7954 (pp30) REVERT: E 73 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8005 (tp30) REVERT: E 85 GLN cc_start: 0.8529 (mt0) cc_final: 0.7775 (mt0) REVERT: E 105 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7452 (tm-30) REVERT: E 113 HIS cc_start: 0.7898 (t70) cc_final: 0.7679 (t70) REVERT: E 115 LYS cc_start: 0.9016 (ttmm) cc_final: 0.8566 (mmmm) REVERT: E 117 VAL cc_start: 0.9449 (t) cc_final: 0.9210 (p) REVERT: E 120 MET cc_start: 0.7465 (mtt) cc_final: 0.6796 (mpp) REVERT: E 125 GLN cc_start: 0.8641 (mt0) cc_final: 0.8424 (mm-40) outliers start: 48 outliers final: 30 residues processed: 412 average time/residue: 0.3444 time to fit residues: 183.9402 Evaluate side-chains 409 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 376 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 ILE 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 73 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 100 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 51 ILE 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 K residue 65 LYS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE 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 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 84 GLN G 73 ASN G 89 ASN G 112 GLN H 92 GLN K 78 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.141182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.098330 restraints weight = 29787.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101489 restraints weight = 16340.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.103511 restraints weight = 11265.973| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13814 Z= 0.174 Angle : 0.658 12.664 19943 Z= 0.374 Chirality : 0.036 0.208 2253 Planarity : 0.005 0.061 1485 Dihedral : 29.559 152.323 4239 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.47 % Allowed : 30.43 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.28), residues: 831 helix: 0.63 (0.22), residues: 533 sheet: -3.84 (1.45), residues: 10 loop : -0.93 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 82 HIS 0.004 0.001 HIS E 113 PHE 0.030 0.002 PHE A 67 TYR 0.018 0.001 TYR D 37 ARG 0.009 0.001 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.05232 ( 658) hydrogen bonds : angle 3.16172 ( 1637) covalent geometry : bond 0.00392 (13814) covalent geometry : angle 0.65850 (19943) *********************** 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 431 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 392 time to evaluate : 1.373 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 25 ASN cc_start: 0.8846 (m110) cc_final: 0.8542 (m-40) REVERT: B 31 LYS cc_start: 0.9376 (ttmt) cc_final: 0.9101 (tptp) REVERT: B 35 ARG cc_start: 0.9228 (mtp85) cc_final: 0.8900 (ttm110) REVERT: B 45 ARG cc_start: 0.9047 (mtp-110) cc_final: 0.8753 (mtp85) REVERT: B 55 ARG cc_start: 0.8565 (mtt90) cc_final: 0.8239 (ttm110) REVERT: B 63 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 79 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8853 (mmmm) REVERT: C 24 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8107 (mm110) REVERT: C 29 ARG cc_start: 0.8585 (tpp80) cc_final: 0.7724 (tpp80) REVERT: C 32 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7508 (tmm-80) REVERT: C 36 LYS cc_start: 0.8721 (ptpp) cc_final: 0.8332 (ptpp) REVERT: C 71 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7697 (ttp-110) REVERT: C 75 LYS cc_start: 0.9284 (mmtm) cc_final: 0.8940 (mmmm) REVERT: C 89 ASN cc_start: 0.8609 (m110) cc_final: 0.8224 (m-40) REVERT: C 110 ASN cc_start: 0.9043 (t0) cc_final: 0.8707 (t0) REVERT: C 115 LEU cc_start: 0.8961 (mt) cc_final: 0.8568 (mm) REVERT: C 116 LEU cc_start: 0.8994 (tp) cc_final: 0.8716 (mt) REVERT: D 31 LYS cc_start: 0.8455 (mppt) cc_final: 0.8243 (mppt) REVERT: D 49 THR cc_start: 0.8748 (m) cc_final: 0.8344 (p) REVERT: D 59 MET cc_start: 0.9653 (mmm) cc_final: 0.9427 (tpp) REVERT: D 64 ASN cc_start: 0.8758 (m-40) cc_final: 0.8542 (m110) REVERT: D 73 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8951 (mm-30) REVERT: D 83 ARG cc_start: 0.8121 (mmt90) cc_final: 0.7799 (mmt90) REVERT: D 92 GLN cc_start: 0.8398 (pt0) cc_final: 0.7524 (pp30) REVERT: D 102 GLU cc_start: 0.7927 (tp30) cc_final: 0.7573 (tp30) REVERT: D 105 LYS cc_start: 0.8783 (tptp) cc_final: 0.8363 (tptp) REVERT: D 109 SER cc_start: 0.9432 (t) cc_final: 0.8863 (p) REVERT: D 110 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8110 (mt-10) REVERT: D 113 LYS cc_start: 0.8959 (mmtm) cc_final: 0.8672 (mmtm) REVERT: D 117 LYS cc_start: 0.9251 (ttpt) cc_final: 0.8987 (pttp) REVERT: F 25 ASN cc_start: 0.8639 (m-40) cc_final: 0.8422 (m-40) REVERT: F 31 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.7947 (tppp) REVERT: F 44 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8190 (mtmm) REVERT: F 45 ARG cc_start: 0.9239 (mtp180) cc_final: 0.8237 (mmm-85) REVERT: F 53 GLU cc_start: 0.8457 (tp30) cc_final: 0.7929 (tp30) REVERT: F 63 GLU cc_start: 0.8035 (pt0) cc_final: 0.7792 (pp20) REVERT: F 88 TYR cc_start: 0.9316 (m-10) cc_final: 0.8835 (m-80) REVERT: G 39 TYR cc_start: 0.9160 (m-80) cc_final: 0.8892 (m-80) REVERT: G 61 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7951 (mm-30) REVERT: G 64 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7511 (tm-30) REVERT: G 68 ASN cc_start: 0.8385 (p0) cc_final: 0.7905 (p0) REVERT: G 78 ILE cc_start: 0.8865 (mt) cc_final: 0.8530 (mt) REVERT: G 104 GLN cc_start: 0.8859 (mp10) cc_final: 0.8652 (mp10) REVERT: H 40 LYS cc_start: 0.9380 (tppt) cc_final: 0.8802 (tppt) REVERT: H 43 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8224 (pptt) REVERT: H 44 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8219 (mm-40) REVERT: H 48 ASP cc_start: 0.8506 (m-30) cc_final: 0.8293 (p0) REVERT: H 56 MET cc_start: 0.7987 (tmm) cc_final: 0.7706 (tmm) REVERT: H 102 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8323 (mm-30) REVERT: H 105 LYS cc_start: 0.9205 (ptmm) cc_final: 0.8591 (pttm) REVERT: A 49 ARG cc_start: 0.8886 (ttm110) cc_final: 0.8483 (mtp-110) REVERT: A 76 GLN cc_start: 0.8778 (mm110) cc_final: 0.8514 (mm-40) REVERT: A 79 LYS cc_start: 0.9135 (tptp) cc_final: 0.8714 (tptp) REVERT: E 39 HIS cc_start: 0.7378 (p-80) cc_final: 0.7060 (p-80) REVERT: E 50 GLU cc_start: 0.8156 (pt0) cc_final: 0.7938 (pt0) REVERT: E 53 ARG cc_start: 0.8248 (tpt90) cc_final: 0.7423 (tpt90) REVERT: E 57 SER cc_start: 0.8587 (p) cc_final: 0.8344 (m) REVERT: E 60 LEU cc_start: 0.9087 (mm) cc_final: 0.8081 (mm) REVERT: E 67 PHE cc_start: 0.8833 (t80) cc_final: 0.8146 (t80) REVERT: E 68 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7906 (pp30) REVERT: E 73 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: E 85 GLN cc_start: 0.8435 (mt0) cc_final: 0.7591 (mt0) REVERT: E 90 MET cc_start: 0.9307 (mmp) cc_final: 0.9099 (mmp) REVERT: E 93 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7245 (tm-30) REVERT: E 94 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8466 (mt-10) REVERT: E 97 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8559 (mt-10) REVERT: E 105 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7507 (tm-30) REVERT: E 113 HIS cc_start: 0.8146 (t70) cc_final: 0.7674 (t-90) REVERT: E 115 LYS cc_start: 0.8975 (ttmm) cc_final: 0.8571 (mmmm) REVERT: E 117 VAL cc_start: 0.9448 (t) cc_final: 0.9194 (p) REVERT: E 120 MET cc_start: 0.7510 (mtt) cc_final: 0.7066 (mpp) outliers start: 39 outliers final: 28 residues processed: 403 average time/residue: 0.3491 time to fit residues: 182.4714 Evaluate side-chains 408 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 377 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE 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 91 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR 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 19 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE 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 G residue 100 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 119 ILE 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 44 optimal weight: 0.0050 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 G 112 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.139716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096956 restraints weight = 30238.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100139 restraints weight = 16606.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102188 restraints weight = 11423.285| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 : 0.004 0.038 13814 Z= 0.178 Angle : 0.647 13.211 19943 Z= 0.367 Chirality : 0.036 0.203 2253 Planarity : 0.005 0.061 1485 Dihedral : 29.513 150.448 4237 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.47 % Allowed : 32.12 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.28), residues: 831 helix: 0.92 (0.23), residues: 532 sheet: -3.72 (1.46), residues: 10 loop : -0.79 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 82 HIS 0.004 0.001 HIS E 113 PHE 0.015 0.002 PHE B 100 TYR 0.016 0.001 TYR G 57 ARG 0.007 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.05168 ( 658) hydrogen bonds : angle 3.19050 ( 1637) covalent geometry : bond 0.00401 (13814) covalent geometry : angle 0.64697 (19943) *********************** 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 421 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 382 time to evaluate : 1.018 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: B 31 LYS cc_start: 0.9418 (ttmt) cc_final: 0.9139 (ttmm) REVERT: B 35 ARG cc_start: 0.9172 (mtp85) cc_final: 0.8795 (ttm110) REVERT: B 45 ARG cc_start: 0.9118 (mtp-110) cc_final: 0.8820 (mtp85) REVERT: B 55 ARG cc_start: 0.8630 (mtt90) cc_final: 0.8282 (ttm110) REVERT: B 63 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7728 (mt-10) REVERT: B 73 THR cc_start: 0.9435 (t) cc_final: 0.9205 (t) REVERT: B 79 LYS cc_start: 0.9286 (mmtp) cc_final: 0.8659 (mmmm) REVERT: B 88 TYR cc_start: 0.8990 (m-10) cc_final: 0.7980 (m-10) REVERT: C 17 ARG cc_start: 0.8976 (mtm180) cc_final: 0.8483 (mtp180) REVERT: C 20 ARG cc_start: 0.8612 (mmt90) cc_final: 0.8269 (mpt-90) REVERT: C 24 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8125 (mm110) REVERT: C 29 ARG cc_start: 0.7974 (tpp80) cc_final: 0.6621 (tpp80) REVERT: C 32 ARG cc_start: 0.8091 (ttp80) cc_final: 0.6499 (tmm-80) REVERT: C 36 LYS cc_start: 0.8646 (ptpp) cc_final: 0.8236 (pttm) REVERT: C 71 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7803 (ttp-110) REVERT: C 84 GLN cc_start: 0.9272 (tp-100) cc_final: 0.9009 (tp-100) REVERT: C 89 ASN cc_start: 0.8572 (m110) cc_final: 0.8167 (m110) REVERT: C 110 ASN cc_start: 0.9180 (t0) cc_final: 0.8882 (t0) REVERT: C 115 LEU cc_start: 0.8987 (mt) cc_final: 0.8472 (tp) REVERT: C 116 LEU cc_start: 0.9071 (tp) cc_final: 0.8762 (mt) REVERT: D 31 LYS cc_start: 0.8522 (mppt) cc_final: 0.8237 (mppt) REVERT: D 39 TYR cc_start: 0.8181 (t80) cc_final: 0.7591 (t80) REVERT: D 59 MET cc_start: 0.9624 (mmm) cc_final: 0.9380 (tpp) REVERT: D 64 ASN cc_start: 0.8862 (m-40) cc_final: 0.8388 (m110) REVERT: D 92 GLN cc_start: 0.8460 (pt0) cc_final: 0.7644 (pp30) REVERT: D 102 GLU cc_start: 0.7969 (tp30) cc_final: 0.7580 (tp30) REVERT: D 105 LYS cc_start: 0.8811 (tptp) cc_final: 0.8356 (tptp) REVERT: D 109 SER cc_start: 0.9389 (t) cc_final: 0.8818 (p) REVERT: D 113 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8578 (mmtm) REVERT: D 117 LYS cc_start: 0.9252 (ttpt) cc_final: 0.8930 (ptmt) REVERT: F 44 LYS cc_start: 0.8906 (mtmm) cc_final: 0.8266 (mtmm) REVERT: F 63 GLU cc_start: 0.8101 (pt0) cc_final: 0.7803 (pp20) REVERT: F 88 TYR cc_start: 0.9344 (m-10) cc_final: 0.8805 (m-80) REVERT: F 90 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9127 (mp) REVERT: G 42 ARG cc_start: 0.8627 (mtm110) cc_final: 0.7649 (mtm180) REVERT: G 61 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8121 (mm-30) REVERT: G 64 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7446 (tm-30) REVERT: G 68 ASN cc_start: 0.8387 (p0) cc_final: 0.7798 (p0) REVERT: G 78 ILE cc_start: 0.8961 (mt) cc_final: 0.8592 (mm) REVERT: G 84 GLN cc_start: 0.9344 (tp-100) cc_final: 0.9005 (tp-100) REVERT: G 95 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8833 (pttm) REVERT: H 40 LYS cc_start: 0.9339 (tppt) cc_final: 0.8814 (tppt) REVERT: H 44 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8364 (mm-40) REVERT: H 48 ASP cc_start: 0.8511 (m-30) cc_final: 0.8154 (p0) REVERT: H 73 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.7565 (mm-30) REVERT: H 117 LYS cc_start: 0.9079 (tppt) cc_final: 0.8628 (tptp) REVERT: A 49 ARG cc_start: 0.8905 (ttm110) cc_final: 0.8368 (mtm-85) REVERT: A 76 GLN cc_start: 0.8761 (mm110) cc_final: 0.8507 (mm-40) REVERT: A 79 LYS cc_start: 0.9180 (tptp) cc_final: 0.8849 (tptp) REVERT: E 39 HIS cc_start: 0.7615 (p-80) cc_final: 0.7272 (p-80) REVERT: E 53 ARG cc_start: 0.8455 (tpt90) cc_final: 0.7823 (tpt90) REVERT: E 57 SER cc_start: 0.8667 (p) cc_final: 0.7528 (p) REVERT: E 60 LEU cc_start: 0.9019 (mm) cc_final: 0.7969 (mm) REVERT: E 67 PHE cc_start: 0.8945 (t80) cc_final: 0.8243 (t80) REVERT: E 68 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7986 (pp30) REVERT: E 73 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8132 (tp30) REVERT: E 76 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8830 (tm-30) REVERT: E 81 ASP cc_start: 0.8392 (m-30) cc_final: 0.8094 (m-30) REVERT: E 85 GLN cc_start: 0.8555 (mt0) cc_final: 0.8299 (mt0) REVERT: E 87 SER cc_start: 0.9230 (m) cc_final: 0.9006 (p) REVERT: E 90 MET cc_start: 0.9344 (mmp) cc_final: 0.9116 (mmp) REVERT: E 93 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7429 (tm-30) REVERT: E 97 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8229 (mt-10) REVERT: E 105 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7529 (tm-30) REVERT: E 115 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8532 (mmmm) REVERT: E 117 VAL cc_start: 0.9478 (t) cc_final: 0.9257 (p) REVERT: E 125 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8283 (mp10) outliers start: 39 outliers final: 27 residues processed: 395 average time/residue: 0.3391 time to fit residues: 174.1805 Evaluate side-chains 396 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 365 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR 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 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 95 LYS Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 42 LEU 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 110 GLU 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 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 73 ASN G 73 ASN G 89 ASN G 112 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.138856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.096023 restraints weight = 30782.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099171 restraints weight = 16907.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101198 restraints weight = 11665.864| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13814 Z= 0.189 Angle : 0.668 15.072 19943 Z= 0.375 Chirality : 0.037 0.208 2253 Planarity : 0.005 0.058 1485 Dihedral : 29.594 150.042 4237 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 6.73 % Allowed : 34.08 % Favored : 59.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.28), residues: 831 helix: 1.13 (0.23), residues: 528 sheet: -3.56 (1.50), residues: 10 loop : -0.73 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.005 0.001 HIS E 113 PHE 0.016 0.001 PHE B 100 TYR 0.033 0.002 TYR D 80 ARG 0.016 0.001 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.05192 ( 658) hydrogen bonds : angle 3.24014 ( 1637) covalent geometry : bond 0.00428 (13814) covalent geometry : angle 0.66770 (19943) *********************** 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 427 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 379 time to evaluate : 0.901 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: B 35 ARG cc_start: 0.9208 (mtp85) cc_final: 0.8813 (ttm110) REVERT: B 44 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9092 (mttt) REVERT: B 63 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7677 (mt-10) REVERT: B 79 LYS cc_start: 0.9196 (mmtp) cc_final: 0.8707 (mmmm) REVERT: C 17 ARG cc_start: 0.8998 (mtm180) cc_final: 0.8508 (mtp180) REVERT: C 20 ARG cc_start: 0.8599 (mmt90) cc_final: 0.8373 (mpt-90) REVERT: C 24 GLN cc_start: 0.8950 (mm-40) cc_final: 0.7991 (mm-40) REVERT: C 29 ARG cc_start: 0.8204 (tpp80) cc_final: 0.6781 (tpp80) REVERT: C 32 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7104 (tmm-80) REVERT: C 71 ARG cc_start: 0.8332 (ttm110) cc_final: 0.7868 (ttp-110) REVERT: C 75 LYS cc_start: 0.9175 (mmtm) cc_final: 0.8781 (mmmm) REVERT: C 84 GLN cc_start: 0.9274 (tp-100) cc_final: 0.9018 (tp-100) REVERT: C 89 ASN cc_start: 0.8571 (m110) cc_final: 0.8198 (m110) REVERT: C 110 ASN cc_start: 0.9220 (t0) cc_final: 0.8901 (t0) REVERT: C 115 LEU cc_start: 0.8991 (mt) cc_final: 0.8405 (tp) REVERT: C 116 LEU cc_start: 0.9143 (tp) cc_final: 0.8886 (mt) REVERT: D 31 LYS cc_start: 0.8480 (mppt) cc_final: 0.8039 (mmtm) REVERT: D 43 LYS cc_start: 0.9217 (mmmt) cc_final: 0.9009 (tppt) REVERT: D 64 ASN cc_start: 0.8884 (m-40) cc_final: 0.8396 (m110) REVERT: D 73 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8440 (mm-30) REVERT: D 76 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7819 (ttp80) REVERT: D 89 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7768 (mtp-110) REVERT: D 92 GLN cc_start: 0.8492 (pt0) cc_final: 0.7694 (pp30) REVERT: D 102 GLU cc_start: 0.8015 (tp30) cc_final: 0.7762 (tp30) REVERT: D 105 LYS cc_start: 0.8670 (tptp) cc_final: 0.7957 (tptp) REVERT: D 110 GLU cc_start: 0.8930 (tt0) cc_final: 0.8432 (mt-10) REVERT: D 117 LYS cc_start: 0.9276 (ttpt) cc_final: 0.8943 (ptmt) REVERT: F 44 LYS cc_start: 0.8874 (mtmm) cc_final: 0.8209 (mtmm) REVERT: F 63 GLU cc_start: 0.8177 (pt0) cc_final: 0.7792 (pp20) REVERT: F 88 TYR cc_start: 0.9390 (m-10) cc_final: 0.8816 (m-80) REVERT: F 90 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9111 (mp) REVERT: G 17 ARG cc_start: 0.9038 (mtm180) cc_final: 0.7542 (ptp-170) REVERT: G 42 ARG cc_start: 0.8645 (mtm110) cc_final: 0.8349 (mtm180) REVERT: G 61 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8125 (mm-30) REVERT: G 64 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7418 (tm-30) REVERT: G 68 ASN cc_start: 0.8494 (p0) cc_final: 0.7912 (p0) REVERT: G 78 ILE cc_start: 0.9098 (mt) cc_final: 0.8645 (mm) REVERT: G 81 ARG cc_start: 0.9043 (tpt90) cc_final: 0.8186 (tpt90) REVERT: G 84 GLN cc_start: 0.9206 (tp-100) cc_final: 0.8832 (tp-100) REVERT: G 85 LEU cc_start: 0.9470 (mt) cc_final: 0.9185 (mt) REVERT: G 95 LYS cc_start: 0.9066 (pttm) cc_final: 0.8842 (pttm) REVERT: H 32 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7990 (tp30) REVERT: H 33 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8520 (t) REVERT: H 40 LYS cc_start: 0.9335 (tppt) cc_final: 0.8807 (tppt) REVERT: H 44 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8314 (mm-40) REVERT: H 48 ASP cc_start: 0.8504 (m-30) cc_final: 0.8206 (p0) REVERT: H 77 LEU cc_start: 0.9211 (mt) cc_final: 0.8955 (mt) REVERT: H 89 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7450 (ptm-80) REVERT: H 99 LEU cc_start: 0.9063 (mt) cc_final: 0.8851 (mp) REVERT: H 113 LYS cc_start: 0.9307 (mtmt) cc_final: 0.8980 (ptpt) REVERT: A 49 ARG cc_start: 0.8983 (ttm110) cc_final: 0.8490 (mtp-110) REVERT: A 76 GLN cc_start: 0.8842 (mm110) cc_final: 0.8499 (mm-40) REVERT: A 79 LYS cc_start: 0.9198 (tptp) cc_final: 0.8579 (tptp) REVERT: E 39 HIS cc_start: 0.7612 (p-80) cc_final: 0.7316 (p-80) REVERT: E 53 ARG cc_start: 0.8545 (tpt90) cc_final: 0.8188 (tpt90) REVERT: E 56 LYS cc_start: 0.8382 (mmtm) cc_final: 0.7986 (mmtm) REVERT: E 57 SER cc_start: 0.8745 (p) cc_final: 0.8324 (p) REVERT: E 60 LEU cc_start: 0.9025 (mm) cc_final: 0.7905 (mm) REVERT: E 67 PHE cc_start: 0.9044 (t80) cc_final: 0.8274 (t80) REVERT: E 73 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: E 76 GLN cc_start: 0.9274 (tm-30) cc_final: 0.8848 (tm-30) REVERT: E 81 ASP cc_start: 0.8602 (m-30) cc_final: 0.8324 (m-30) REVERT: E 87 SER cc_start: 0.9265 (m) cc_final: 0.9044 (p) REVERT: E 90 MET cc_start: 0.9216 (mmp) cc_final: 0.9007 (mmp) REVERT: E 93 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7171 (tm-30) REVERT: E 94 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8127 (mt-10) REVERT: E 97 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8253 (mt-10) REVERT: E 99 TYR cc_start: 0.9036 (t80) cc_final: 0.8785 (t80) REVERT: E 105 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7601 (tm-30) REVERT: E 115 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8573 (mmmm) REVERT: E 117 VAL cc_start: 0.9500 (t) cc_final: 0.9281 (p) outliers start: 48 outliers final: 37 residues processed: 392 average time/residue: 0.3695 time to fit residues: 190.7685 Evaluate side-chains 413 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 371 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 44 LYS 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 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR 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 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 63 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 33 SER 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 90 GLU Chi-restraints excluded: chain H residue 103 LEU 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 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 71 VAL 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: 0.8980 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 G 112 GLN A 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.139694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097084 restraints weight = 30692.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100193 restraints weight = 16897.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102312 restraints weight = 11669.587| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13814 Z= 0.176 Angle : 0.665 14.283 19943 Z= 0.373 Chirality : 0.036 0.206 2253 Planarity : 0.005 0.063 1485 Dihedral : 29.579 149.485 4237 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.75 % Allowed : 36.33 % Favored : 57.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.28), residues: 831 helix: 1.24 (0.23), residues: 517 sheet: -3.47 (1.52), residues: 10 loop : -0.75 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.005 0.001 HIS E 113 PHE 0.018 0.001 PHE B 100 TYR 0.031 0.002 TYR D 80 ARG 0.009 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.05037 ( 658) hydrogen bonds : angle 3.25578 ( 1637) covalent geometry : bond 0.00399 (13814) covalent geometry : angle 0.66531 (19943) *********************** 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 430 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 389 time to evaluate : 0.933 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: B 31 LYS cc_start: 0.9506 (ttmt) cc_final: 0.8943 (tptp) REVERT: B 35 ARG cc_start: 0.9203 (mtp85) cc_final: 0.8840 (ttm110) REVERT: B 44 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8971 (mttt) REVERT: B 63 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7779 (mt-10) REVERT: B 79 LYS cc_start: 0.9166 (mmtp) cc_final: 0.8686 (mmmm) REVERT: C 17 ARG cc_start: 0.9000 (mtm180) cc_final: 0.8469 (mtp180) REVERT: C 20 ARG cc_start: 0.8635 (mmt90) cc_final: 0.8307 (mpt-90) REVERT: C 24 GLN cc_start: 0.8940 (mm-40) cc_final: 0.7981 (mm-40) REVERT: C 29 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7272 (tpp80) REVERT: C 32 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7726 (tmm-80) REVERT: C 34 LEU cc_start: 0.8668 (mt) cc_final: 0.8407 (mt) REVERT: C 36 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8187 (mtmm) REVERT: C 75 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8806 (mmmm) REVERT: C 84 GLN cc_start: 0.9244 (tp-100) cc_final: 0.8955 (tp40) REVERT: C 108 LEU cc_start: 0.8726 (mt) cc_final: 0.8144 (tt) REVERT: C 110 ASN cc_start: 0.9147 (t0) cc_final: 0.8908 (t0) REVERT: C 115 LEU cc_start: 0.8979 (mt) cc_final: 0.8373 (tp) REVERT: C 116 LEU cc_start: 0.9156 (tp) cc_final: 0.8885 (mt) REVERT: D 31 LYS cc_start: 0.8639 (mppt) cc_final: 0.8246 (mmtm) REVERT: D 39 TYR cc_start: 0.8234 (t80) cc_final: 0.7629 (t80) REVERT: D 43 LYS cc_start: 0.9221 (mmmt) cc_final: 0.8940 (tppt) REVERT: D 64 ASN cc_start: 0.8889 (m-40) cc_final: 0.8414 (m110) REVERT: D 73 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8540 (mm-30) REVERT: D 89 ARG cc_start: 0.8089 (mtp-110) cc_final: 0.7677 (mtp-110) REVERT: D 92 GLN cc_start: 0.8482 (pt0) cc_final: 0.7673 (pp30) REVERT: D 102 GLU cc_start: 0.8144 (tp30) cc_final: 0.7823 (tp30) REVERT: D 105 LYS cc_start: 0.8566 (tptp) cc_final: 0.8058 (tptp) REVERT: D 110 GLU cc_start: 0.8922 (tt0) cc_final: 0.8339 (mt-10) REVERT: D 117 LYS cc_start: 0.9267 (ttpt) cc_final: 0.8977 (ptmt) REVERT: F 44 LYS cc_start: 0.8892 (mtmm) cc_final: 0.8175 (mtmm) REVERT: F 63 GLU cc_start: 0.8197 (pt0) cc_final: 0.7810 (pp20) REVERT: F 88 TYR cc_start: 0.9362 (m-10) cc_final: 0.8816 (m-80) REVERT: F 90 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9133 (mp) REVERT: G 20 ARG cc_start: 0.8215 (mtm180) cc_final: 0.7819 (ptt180) REVERT: G 38 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.7630 (t0) REVERT: G 42 ARG cc_start: 0.8772 (mtm110) cc_final: 0.8094 (mtm180) REVERT: G 61 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8116 (mm-30) REVERT: G 68 ASN cc_start: 0.8452 (p0) cc_final: 0.7941 (p0) REVERT: G 78 ILE cc_start: 0.9095 (mt) cc_final: 0.8638 (mm) REVERT: G 79 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8482 (mm) REVERT: G 81 ARG cc_start: 0.8841 (tpt90) cc_final: 0.8231 (tpt90) REVERT: G 84 GLN cc_start: 0.9342 (tp-100) cc_final: 0.9020 (tp-100) REVERT: G 89 ASN cc_start: 0.8617 (m-40) cc_final: 0.8097 (m-40) REVERT: G 112 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8444 (mm110) REVERT: H 29 THR cc_start: 0.8458 (t) cc_final: 0.8213 (m) REVERT: H 32 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7994 (tp30) REVERT: H 33 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8390 (t) REVERT: H 40 LYS cc_start: 0.9334 (tppt) cc_final: 0.8800 (tppt) REVERT: H 44 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8289 (mm-40) REVERT: H 48 ASP cc_start: 0.8424 (m-30) cc_final: 0.8207 (p0) REVERT: H 77 LEU cc_start: 0.9141 (mt) cc_final: 0.8882 (mt) REVERT: H 89 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7582 (ptm-80) REVERT: H 99 LEU cc_start: 0.9056 (mt) cc_final: 0.8825 (mp) REVERT: H 117 LYS cc_start: 0.9108 (tppt) cc_final: 0.8647 (tptp) REVERT: H 118 TYR cc_start: 0.8323 (t80) cc_final: 0.7551 (t80) REVERT: A 49 ARG cc_start: 0.9033 (ttm110) cc_final: 0.8508 (mtp-110) REVERT: A 76 GLN cc_start: 0.8863 (mm110) cc_final: 0.8621 (mm-40) REVERT: E 39 HIS cc_start: 0.7639 (p-80) cc_final: 0.7382 (p-80) REVERT: E 53 ARG cc_start: 0.8640 (tpt90) cc_final: 0.7687 (tpt90) REVERT: E 56 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8201 (mmtm) REVERT: E 60 LEU cc_start: 0.9054 (mm) cc_final: 0.7806 (mm) REVERT: E 63 ARG cc_start: 0.7562 (mmp80) cc_final: 0.7101 (mmp80) REVERT: E 67 PHE cc_start: 0.8966 (t80) cc_final: 0.8063 (t80) REVERT: E 68 GLN cc_start: 0.8377 (pp30) cc_final: 0.8079 (pp30) REVERT: E 73 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8265 (tp30) REVERT: E 76 GLN cc_start: 0.9316 (tm-30) cc_final: 0.8849 (tm-30) REVERT: E 81 ASP cc_start: 0.8573 (m-30) cc_final: 0.8311 (m-30) REVERT: E 90 MET cc_start: 0.9287 (mmp) cc_final: 0.9044 (mmp) REVERT: E 93 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7245 (tm-30) REVERT: E 97 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8186 (mt-10) REVERT: E 105 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7650 (tm-30) REVERT: E 115 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8554 (mmmm) REVERT: E 117 VAL cc_start: 0.9505 (t) cc_final: 0.9277 (p) outliers start: 41 outliers final: 28 residues processed: 402 average time/residue: 0.3635 time to fit residues: 187.7752 Evaluate side-chains 409 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 373 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LYS 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 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR 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 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 38 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** C 73 ASN C 89 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.139373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.096905 restraints weight = 30845.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.100098 restraints weight = 17049.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.102174 restraints weight = 11737.416| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13814 Z= 0.178 Angle : 0.694 15.758 19943 Z= 0.385 Chirality : 0.037 0.210 2253 Planarity : 0.005 0.060 1485 Dihedral : 29.619 148.830 4237 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.75 % Allowed : 38.43 % Favored : 55.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.28), residues: 831 helix: 1.21 (0.23), residues: 515 sheet: -3.50 (1.40), residues: 10 loop : -0.74 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.005 0.001 HIS G 31 PHE 0.010 0.001 PHE F 61 TYR 0.052 0.002 TYR D 80 ARG 0.013 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.05017 ( 658) hydrogen bonds : angle 3.30826 ( 1637) covalent geometry : bond 0.00408 (13814) covalent geometry : angle 0.69363 (19943) *********************** 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 418 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 377 time to evaluate : 1.004 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: 0.9188 (mtp85) cc_final: 0.8831 (ttm110) REVERT: B 39 ARG cc_start: 0.9192 (mmt90) cc_final: 0.8932 (tpp-160) REVERT: B 44 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8668 (mttt) REVERT: B 63 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7797 (mt-10) REVERT: B 79 LYS cc_start: 0.9115 (mmtp) cc_final: 0.8637 (mmmm) REVERT: C 17 ARG cc_start: 0.9190 (mtm180) cc_final: 0.8686 (mtp180) REVERT: C 20 ARG cc_start: 0.8654 (mmt90) cc_final: 0.8438 (mpt-90) REVERT: C 24 GLN cc_start: 0.8953 (mm-40) cc_final: 0.7754 (mm-40) REVERT: C 25 PHE cc_start: 0.8883 (m-10) cc_final: 0.8406 (m-10) REVERT: C 29 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7237 (tpp80) REVERT: C 32 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7597 (tmm-80) REVERT: C 34 LEU cc_start: 0.8614 (mt) cc_final: 0.8317 (mt) REVERT: C 35 ARG cc_start: 0.8238 (tpp-160) cc_final: 0.7764 (mmt-90) REVERT: C 36 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8122 (mtmm) REVERT: C 43 VAL cc_start: 0.8840 (p) cc_final: 0.8636 (p) REVERT: C 56 GLU cc_start: 0.8686 (tt0) cc_final: 0.8299 (mm-30) REVERT: C 75 LYS cc_start: 0.9075 (mmtm) cc_final: 0.8834 (mmmm) REVERT: C 89 ASN cc_start: 0.8643 (m-40) cc_final: 0.8426 (m-40) REVERT: C 116 LEU cc_start: 0.9208 (tp) cc_final: 0.9001 (mt) REVERT: D 31 LYS cc_start: 0.8604 (mppt) cc_final: 0.8174 (mmtm) REVERT: D 39 TYR cc_start: 0.8323 (t80) cc_final: 0.7744 (t80) REVERT: D 43 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8963 (tppt) REVERT: D 64 ASN cc_start: 0.8886 (m-40) cc_final: 0.8411 (m110) REVERT: D 73 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8588 (mm-30) REVERT: D 76 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7779 (ttp-110) REVERT: D 89 ARG cc_start: 0.8019 (mtp-110) cc_final: 0.7604 (mtp-110) REVERT: D 92 GLN cc_start: 0.8449 (pt0) cc_final: 0.7688 (pp30) REVERT: D 102 GLU cc_start: 0.8140 (tp30) cc_final: 0.7861 (tp30) REVERT: D 105 LYS cc_start: 0.8582 (tptp) cc_final: 0.8093 (tptp) REVERT: D 110 GLU cc_start: 0.8890 (tt0) cc_final: 0.8358 (mt-10) REVERT: D 117 LYS cc_start: 0.9275 (ttpt) cc_final: 0.8977 (ptmt) REVERT: F 44 LYS cc_start: 0.8858 (mtmm) cc_final: 0.8605 (mtmm) REVERT: F 53 GLU cc_start: 0.8007 (tp30) cc_final: 0.7782 (tp30) REVERT: F 63 GLU cc_start: 0.8197 (pt0) cc_final: 0.7875 (pp20) REVERT: F 78 ARG cc_start: 0.8642 (tpp80) cc_final: 0.7893 (tpp80) REVERT: F 80 THR cc_start: 0.9255 (p) cc_final: 0.9016 (p) REVERT: F 88 TYR cc_start: 0.9363 (m-10) cc_final: 0.8800 (m-80) REVERT: F 90 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9077 (mp) REVERT: G 20 ARG cc_start: 0.8257 (mtm180) cc_final: 0.7841 (ptt180) REVERT: G 38 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.7804 (t0) REVERT: G 42 ARG cc_start: 0.8664 (mtm110) cc_final: 0.7840 (mtm180) REVERT: G 61 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8108 (mm-30) REVERT: G 68 ASN cc_start: 0.8442 (p0) cc_final: 0.8154 (p0) REVERT: G 78 ILE cc_start: 0.9095 (mt) cc_final: 0.8631 (mm) REVERT: G 79 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8430 (mm) REVERT: G 81 ARG cc_start: 0.8721 (tpt90) cc_final: 0.8273 (tpt90) REVERT: G 84 GLN cc_start: 0.9328 (tp-100) cc_final: 0.9053 (tp-100) REVERT: G 89 ASN cc_start: 0.8571 (m-40) cc_final: 0.7826 (m110) REVERT: G 112 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8481 (mm110) REVERT: H 40 LYS cc_start: 0.9328 (tppt) cc_final: 0.8737 (tppt) REVERT: H 44 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8202 (mm110) REVERT: H 77 LEU cc_start: 0.9137 (mt) cc_final: 0.8835 (mt) REVERT: H 89 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7413 (ptm-80) REVERT: H 99 LEU cc_start: 0.9161 (mt) cc_final: 0.8926 (mp) REVERT: H 117 LYS cc_start: 0.9243 (tppt) cc_final: 0.8764 (tptp) REVERT: A 41 TYR cc_start: 0.9011 (m-80) cc_final: 0.8737 (m-80) REVERT: A 49 ARG cc_start: 0.9015 (ttm110) cc_final: 0.8582 (mtp-110) REVERT: A 56 LYS cc_start: 0.8718 (pttp) cc_final: 0.8375 (pttp) REVERT: A 76 GLN cc_start: 0.8872 (mm110) cc_final: 0.8529 (mm-40) REVERT: E 39 HIS cc_start: 0.7622 (p-80) cc_final: 0.7417 (p-80) REVERT: E 55 GLN cc_start: 0.8928 (tt0) cc_final: 0.8658 (tt0) REVERT: E 56 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8040 (mmtm) REVERT: E 57 SER cc_start: 0.8823 (m) cc_final: 0.8429 (p) REVERT: E 60 LEU cc_start: 0.9003 (mm) cc_final: 0.8044 (mp) REVERT: E 63 ARG cc_start: 0.7735 (mmp80) cc_final: 0.7383 (mmp80) REVERT: E 67 PHE cc_start: 0.9018 (t80) cc_final: 0.8484 (t80) REVERT: E 68 GLN cc_start: 0.8392 (pp30) cc_final: 0.7951 (pp30) REVERT: E 76 GLN cc_start: 0.9304 (tm-30) cc_final: 0.8804 (tm-30) REVERT: E 81 ASP cc_start: 0.8368 (m-30) cc_final: 0.8151 (m-30) REVERT: E 93 GLN cc_start: 0.8307 (tm-30) cc_final: 0.6967 (tm-30) REVERT: E 99 TYR cc_start: 0.9039 (t80) cc_final: 0.8775 (t80) REVERT: E 105 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7681 (tm-30) REVERT: E 115 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8502 (mmmm) REVERT: E 117 VAL cc_start: 0.9506 (t) cc_final: 0.9263 (p) outliers start: 41 outliers final: 33 residues processed: 390 average time/residue: 0.3608 time to fit residues: 184.3879 Evaluate side-chains 411 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 373 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LYS 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 86 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 73 ASN 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 D residue 103 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 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 38 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 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 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** 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 = 0.3988 r_free = 0.3988 target = 0.137100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.094576 restraints weight = 30741.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.097666 restraints weight = 17285.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099682 restraints weight = 12018.795| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.7592 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= 0.231 Angle : 0.741 16.984 19943 Z= 0.409 Chirality : 0.039 0.214 2253 Planarity : 0.006 0.063 1485 Dihedral : 29.729 148.406 4237 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 6.03 % Allowed : 37.31 % Favored : 56.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.28), residues: 831 helix: 0.77 (0.22), residues: 527 sheet: -3.44 (1.33), residues: 10 loop : -0.62 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.007 0.001 HIS E 113 PHE 0.021 0.002 PHE B 100 TYR 0.065 0.003 TYR B 88 ARG 0.017 0.001 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.05477 ( 658) hydrogen bonds : angle 3.56479 ( 1637) covalent geometry : bond 0.00532 (13814) covalent geometry : angle 0.74076 (19943) *********************** 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 417 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 374 time to evaluate : 0.912 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: B 31 LYS cc_start: 0.9385 (ttmt) cc_final: 0.8985 (tptp) REVERT: B 39 ARG cc_start: 0.9161 (mmt90) cc_final: 0.8653 (tpp-160) REVERT: B 44 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9015 (mttt) REVERT: B 63 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7739 (mt-10) REVERT: B 79 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8646 (mmmm) REVERT: B 98 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: C 17 ARG cc_start: 0.9311 (mtm180) cc_final: 0.8802 (mtp180) REVERT: C 20 ARG cc_start: 0.8664 (mmt90) cc_final: 0.8266 (mpt-90) REVERT: C 24 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8097 (mm-40) REVERT: C 29 ARG cc_start: 0.8074 (tpp80) cc_final: 0.7218 (tpp80) REVERT: C 34 LEU cc_start: 0.8627 (mt) cc_final: 0.8342 (mt) REVERT: C 36 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8299 (pttm) REVERT: C 75 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8984 (mmmm) REVERT: C 108 LEU cc_start: 0.8610 (mt) cc_final: 0.8071 (tt) REVERT: C 115 LEU cc_start: 0.8898 (mt) cc_final: 0.7998 (mt) REVERT: D 31 LYS cc_start: 0.8636 (mppt) cc_final: 0.8219 (mmtm) REVERT: D 43 LYS cc_start: 0.9251 (mmmt) cc_final: 0.9024 (tppt) REVERT: D 64 ASN cc_start: 0.8822 (m-40) cc_final: 0.8341 (m110) REVERT: D 73 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8375 (mm-30) REVERT: D 76 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7410 (ttp-110) REVERT: D 89 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7822 (mtp-110) REVERT: D 92 GLN cc_start: 0.8349 (pt0) cc_final: 0.7702 (pp30) REVERT: D 102 GLU cc_start: 0.8146 (tp30) cc_final: 0.7887 (tp30) REVERT: D 105 LYS cc_start: 0.8635 (tptp) cc_final: 0.8041 (tptp) REVERT: D 110 GLU cc_start: 0.8905 (tt0) cc_final: 0.8373 (mt-10) REVERT: D 117 LYS cc_start: 0.9216 (ttpt) cc_final: 0.9006 (tttt) REVERT: F 44 LYS cc_start: 0.8902 (mtmm) cc_final: 0.8214 (mtmm) REVERT: F 63 GLU cc_start: 0.8199 (pt0) cc_final: 0.7870 (pp20) REVERT: F 88 TYR cc_start: 0.9419 (m-10) cc_final: 0.8817 (m-80) REVERT: F 90 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9112 (mp) REVERT: G 20 ARG cc_start: 0.8232 (mtm180) cc_final: 0.7791 (ptt180) REVERT: G 29 ARG cc_start: 0.8700 (tpp80) cc_final: 0.8103 (tpp80) REVERT: G 38 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.7670 (t0) REVERT: G 42 ARG cc_start: 0.8330 (mtm110) cc_final: 0.7882 (mtm180) REVERT: G 61 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8201 (mm-30) REVERT: G 68 ASN cc_start: 0.8589 (p0) cc_final: 0.8384 (p0) REVERT: G 78 ILE cc_start: 0.9084 (mt) cc_final: 0.8710 (mm) REVERT: G 84 GLN cc_start: 0.9420 (tp-100) cc_final: 0.9086 (tp-100) REVERT: G 89 ASN cc_start: 0.8578 (m-40) cc_final: 0.8277 (p0) REVERT: G 112 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8535 (mm110) REVERT: H 40 LYS cc_start: 0.9290 (tppt) cc_final: 0.8878 (tmtt) REVERT: H 43 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8330 (tmmt) REVERT: H 89 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7742 (ptm-80) REVERT: H 92 GLN cc_start: 0.9369 (tt0) cc_final: 0.9105 (tt0) REVERT: H 113 LYS cc_start: 0.9232 (tptt) cc_final: 0.8765 (tppt) REVERT: H 117 LYS cc_start: 0.9288 (tppt) cc_final: 0.8921 (tptp) REVERT: H 120 SER cc_start: 0.9486 (m) cc_final: 0.9272 (p) REVERT: A 42 ARG cc_start: 0.7812 (mmm-85) cc_final: 0.7423 (mmm160) REVERT: A 49 ARG cc_start: 0.9014 (ttm110) cc_final: 0.8570 (mtp-110) REVERT: A 79 LYS cc_start: 0.9102 (tptp) cc_final: 0.8860 (tptp) REVERT: E 56 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8212 (mmtm) REVERT: E 63 ARG cc_start: 0.7915 (mmp80) cc_final: 0.7680 (mmp80) REVERT: E 68 GLN cc_start: 0.8439 (pp30) cc_final: 0.7768 (pp30) REVERT: E 76 GLN cc_start: 0.9289 (tm-30) cc_final: 0.8799 (tm-30) REVERT: E 81 ASP cc_start: 0.8567 (m-30) cc_final: 0.8337 (m-30) REVERT: E 99 TYR cc_start: 0.9083 (t80) cc_final: 0.8788 (t80) REVERT: E 105 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7665 (tm-30) REVERT: E 115 LYS cc_start: 0.8969 (ttmm) cc_final: 0.8552 (mmmm) REVERT: E 117 VAL cc_start: 0.9367 (t) cc_final: 0.9119 (p) outliers start: 43 outliers final: 32 residues processed: 387 average time/residue: 0.3325 time to fit residues: 168.1418 Evaluate side-chains 401 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 363 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LYS 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 91 LYS Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 97 LEU 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 D residue 103 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 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 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 90 GLU 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 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 51 ILE Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 99 optimal weight: 0.3980 chunk 17 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** 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 = 0.4017 r_free = 0.4017 target = 0.139707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097677 restraints weight = 30574.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100844 restraints weight = 16944.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102854 restraints weight = 11676.261| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.7800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13814 Z= 0.174 Angle : 0.732 17.426 19943 Z= 0.402 Chirality : 0.038 0.219 2253 Planarity : 0.006 0.062 1485 Dihedral : 29.713 148.323 4237 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.07 % Allowed : 40.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.28), residues: 831 helix: 1.06 (0.22), residues: 515 sheet: -3.47 (1.29), residues: 10 loop : -0.73 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.004 0.001 HIS H 46 PHE 0.019 0.001 PHE B 100 TYR 0.096 0.003 TYR B 88 ARG 0.011 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 658) hydrogen bonds : angle 3.41267 ( 1637) covalent geometry : bond 0.00400 (13814) covalent geometry : angle 0.73200 (19943) ********************** 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: 29 poor density : 374 time to evaluate : 0.895 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 35 ARG cc_start: 0.9082 (mtp85) cc_final: 0.8845 (ttm110) REVERT: B 44 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8848 (mttt) REVERT: B 63 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7793 (mt-10) REVERT: B 79 LYS cc_start: 0.9072 (mmtp) cc_final: 0.8599 (mmmm) REVERT: C 17 ARG cc_start: 0.9231 (mtm180) cc_final: 0.8786 (mtt90) REVERT: C 20 ARG cc_start: 0.8665 (mmt90) cc_final: 0.8277 (mpt-90) REVERT: C 24 GLN cc_start: 0.8860 (mm-40) cc_final: 0.7853 (mm-40) REVERT: C 25 PHE cc_start: 0.8961 (m-10) cc_final: 0.8446 (m-10) REVERT: C 29 ARG cc_start: 0.7975 (tpp80) cc_final: 0.7180 (tpp80) REVERT: C 32 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7691 (tmm-80) REVERT: C 34 LEU cc_start: 0.8610 (mt) cc_final: 0.8247 (mt) REVERT: C 35 ARG cc_start: 0.8280 (tpp-160) cc_final: 0.7970 (mmt180) REVERT: C 36 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8170 (mtmm) REVERT: C 56 GLU cc_start: 0.8700 (tt0) cc_final: 0.8317 (mm-30) REVERT: C 75 LYS cc_start: 0.9054 (mmtm) cc_final: 0.8827 (mmmm) REVERT: C 115 LEU cc_start: 0.8918 (mt) cc_final: 0.8273 (mt) REVERT: C 116 LEU cc_start: 0.9122 (tp) cc_final: 0.8822 (mt) REVERT: D 31 LYS cc_start: 0.8682 (mppt) cc_final: 0.8281 (mmtm) REVERT: D 39 TYR cc_start: 0.8265 (t80) cc_final: 0.7750 (t80) REVERT: D 43 LYS cc_start: 0.9235 (mmmt) cc_final: 0.9019 (tppt) REVERT: D 64 ASN cc_start: 0.8876 (m-40) cc_final: 0.8470 (m110) REVERT: D 73 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8265 (mm-30) REVERT: D 76 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7498 (ttp-110) REVERT: D 92 GLN cc_start: 0.8300 (pt0) cc_final: 0.7643 (pp30) REVERT: D 102 GLU cc_start: 0.8126 (tp30) cc_final: 0.7813 (tp30) REVERT: D 105 LYS cc_start: 0.8656 (tptp) cc_final: 0.8174 (tptp) REVERT: D 110 GLU cc_start: 0.8915 (tt0) cc_final: 0.8363 (mt-10) REVERT: D 117 LYS cc_start: 0.9247 (ttpt) cc_final: 0.9012 (ptmt) REVERT: F 44 LYS cc_start: 0.8844 (mtmm) cc_final: 0.8242 (mtmm) REVERT: F 63 GLU cc_start: 0.8322 (pt0) cc_final: 0.8088 (pp20) REVERT: F 88 TYR cc_start: 0.9255 (m-10) cc_final: 0.8770 (m-80) REVERT: F 90 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9112 (mp) REVERT: G 20 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7819 (ptt180) REVERT: G 29 ARG cc_start: 0.8364 (tpp80) cc_final: 0.7784 (tpp80) REVERT: G 38 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.7844 (t0) REVERT: G 42 ARG cc_start: 0.8370 (mtm110) cc_final: 0.7980 (mtm180) REVERT: G 61 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8156 (mm-30) REVERT: G 68 ASN cc_start: 0.8503 (p0) cc_final: 0.8251 (p0) REVERT: G 78 ILE cc_start: 0.9088 (mt) cc_final: 0.8626 (mm) REVERT: G 79 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8311 (mm) REVERT: G 81 ARG cc_start: 0.8790 (tpt90) cc_final: 0.8350 (tpt90) REVERT: G 84 GLN cc_start: 0.9322 (tp-100) cc_final: 0.9075 (tp-100) REVERT: G 89 ASN cc_start: 0.8595 (m-40) cc_final: 0.8289 (p0) REVERT: G 112 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8470 (mm110) REVERT: H 89 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7572 (ptm-80) REVERT: H 92 GLN cc_start: 0.9313 (tt0) cc_final: 0.8993 (tt0) REVERT: H 102 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8305 (tp30) REVERT: H 105 LYS cc_start: 0.9084 (ptmm) cc_final: 0.7116 (mtmm) REVERT: H 113 LYS cc_start: 0.9199 (tptt) cc_final: 0.8749 (tppt) REVERT: H 117 LYS cc_start: 0.9295 (tppt) cc_final: 0.8909 (tptp) REVERT: H 120 SER cc_start: 0.9474 (m) cc_final: 0.9258 (p) REVERT: A 42 ARG cc_start: 0.7725 (mmm-85) cc_final: 0.7290 (mmm160) REVERT: A 49 ARG cc_start: 0.9025 (ttm110) cc_final: 0.8458 (mtp-110) REVERT: A 76 GLN cc_start: 0.8664 (mm-40) cc_final: 0.7979 (mt0) REVERT: A 120 MET cc_start: 0.7829 (mmm) cc_final: 0.7374 (mtt) REVERT: E 56 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8163 (mptt) REVERT: E 68 GLN cc_start: 0.8177 (pp30) cc_final: 0.7712 (pp30) REVERT: E 76 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8792 (tm-30) REVERT: E 81 ASP cc_start: 0.8483 (m-30) cc_final: 0.8247 (m-30) REVERT: E 93 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7892 (tm-30) REVERT: E 99 TYR cc_start: 0.9058 (t80) cc_final: 0.8669 (t80) REVERT: E 105 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7658 (tm-30) REVERT: E 115 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8492 (mmmm) REVERT: E 117 VAL cc_start: 0.9405 (t) cc_final: 0.9148 (p) outliers start: 29 outliers final: 20 residues processed: 382 average time/residue: 0.3927 time to fit residues: 196.5154 Evaluate side-chains 390 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 365 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 97 LEU 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 D residue 103 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 38 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 84 SER 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 65 LEU Chi-restraints excluded: chain A residue 68 GLN 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 75 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** 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 = 0.4011 r_free = 0.4011 target = 0.139000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097344 restraints weight = 30778.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.100471 restraints weight = 17049.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.102526 restraints weight = 11746.379| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.7955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13814 Z= 0.183 Angle : 0.737 16.255 19943 Z= 0.404 Chirality : 0.038 0.215 2253 Planarity : 0.006 0.061 1485 Dihedral : 29.694 147.650 4237 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.49 % Allowed : 40.53 % Favored : 54.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 831 helix: 0.95 (0.22), residues: 518 sheet: -3.57 (1.23), residues: 10 loop : -0.69 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.004 0.001 HIS E 113 PHE 0.019 0.001 PHE B 100 TYR 0.092 0.003 TYR B 88 ARG 0.014 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.05026 ( 658) hydrogen bonds : angle 3.42724 ( 1637) covalent geometry : bond 0.00424 (13814) covalent geometry : angle 0.73662 (19943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5293.10 seconds wall clock time: 92 minutes 30.34 seconds (5550.34 seconds total)