Starting phenix.real_space_refine on Thu May 15 03:21:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbq_16549/05_2025/8cbq_16549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbq_16549/05_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_16549/05_2025/8cbq_16549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbq_16549/05_2025/8cbq_16549.map" model { file = "/net/cci-nas-00/data/ceres_data/8cbq_16549/05_2025/8cbq_16549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbq_16549/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.17, per 1000 atoms: 0.55 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: 3.00 Conformation dependent library (CDL) restraints added in 968.7 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: 6.41 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: 4.48 Time building geometry restraints manager: 3.48 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: 0.550 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.750 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.120 ------------------------------------------------------------------------------- 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 : 1.080 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: 0.3636 time to fit residues: 218.0577 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 : 1.036 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.148129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106820 restraints weight = 28791.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110399 restraints weight = 14894.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.112689 restraints weight = 9834.124| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 3.52536 ( 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 : 0.938 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: 0.9028 (m110) cc_final: 0.8747 (m110) REVERT: B 79 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8417 (mmtm) REVERT: C 32 ARG cc_start: 0.7910 (ttp80) cc_final: 0.6990 (ttp80) REVERT: C 71 ARG cc_start: 0.7412 (ttm110) cc_final: 0.6932 (ttp-110) REVERT: C 75 LYS cc_start: 0.8408 (mmmm) cc_final: 0.7961 (mmmm) REVERT: C 110 ASN cc_start: 0.8907 (t0) cc_final: 0.8404 (t0) REVERT: C 115 LEU cc_start: 0.9273 (mt) cc_final: 0.9010 (mp) REVERT: D 34 TYR cc_start: 0.8599 (m-80) cc_final: 0.8384 (m-10) REVERT: D 49 THR cc_start: 0.8474 (m) cc_final: 0.8117 (p) REVERT: D 59 MET cc_start: 0.9704 (mmm) cc_final: 0.9111 (tpp) REVERT: D 64 ASN cc_start: 0.8804 (m110) cc_final: 0.8207 (m110) REVERT: D 65 ASP cc_start: 0.8789 (t70) cc_final: 0.8371 (t70) REVERT: D 105 LYS cc_start: 0.8658 (tptp) cc_final: 0.8408 (tptp) REVERT: D 110 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7689 (mt-10) REVERT: D 113 LYS cc_start: 0.9082 (mmtm) cc_final: 0.8801 (mmtm) REVERT: F 25 ASN cc_start: 0.8599 (m-40) cc_final: 0.8065 (m-40) REVERT: F 39 ARG cc_start: 0.9179 (mmt-90) cc_final: 0.8761 (mmt180) REVERT: F 53 GLU cc_start: 0.8529 (tp30) cc_final: 0.7767 (tp30) REVERT: F 75 HIS cc_start: 0.8275 (t70) cc_final: 0.7863 (t70) REVERT: F 79 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8757 (mmtm) REVERT: F 88 TYR cc_start: 0.9274 (m-10) cc_final: 0.8758 (m-80) REVERT: F 92 ARG cc_start: 0.8954 (mmm160) cc_final: 0.8736 (mmm-85) REVERT: G 17 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7705 (ptp-170) REVERT: G 42 ARG cc_start: 0.8658 (mtp-110) cc_final: 0.8188 (mtm-85) REVERT: G 61 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8011 (mm-30) REVERT: G 73 ASN cc_start: 0.8751 (t0) cc_final: 0.8274 (t0) REVERT: G 81 ARG cc_start: 0.8531 (tpt90) cc_final: 0.8254 (tpt90) REVERT: G 101 THR cc_start: 0.9188 (m) cc_final: 0.8933 (p) REVERT: G 110 ASN cc_start: 0.8940 (t0) cc_final: 0.8376 (t0) REVERT: G 112 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8312 (mm110) REVERT: H 34 TYR cc_start: 0.8039 (m-80) cc_final: 0.7466 (m-10) REVERT: H 39 TYR cc_start: 0.8260 (t80) cc_final: 0.7930 (t80) REVERT: H 40 LYS cc_start: 0.8866 (tppt) cc_final: 0.8437 (tppt) REVERT: H 43 LYS cc_start: 0.8537 (pptt) cc_final: 0.7922 (pptt) REVERT: H 44 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8239 (mm-40) REVERT: H 102 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8363 (mm-30) REVERT: K 40 LEU cc_start: 0.4455 (OUTLIER) cc_final: 0.4008 (tp) REVERT: A 40 ARG cc_start: 0.8338 (mtm110) cc_final: 0.8119 (mtp180) REVERT: A 55 GLN cc_start: 0.9264 (mt0) cc_final: 0.8769 (tt0) REVERT: A 56 LYS cc_start: 0.8467 (pttp) cc_final: 0.8080 (pttt) REVERT: A 76 GLN cc_start: 0.8740 (mm110) cc_final: 0.8203 (mm-40) REVERT: A 79 LYS cc_start: 0.8783 (tptp) cc_final: 0.8531 (tptt) REVERT: A 106 ASP cc_start: 0.8793 (m-30) cc_final: 0.8452 (m-30) REVERT: A 129 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8130 (mmp80) REVERT: E 41 TYR cc_start: 0.8135 (m-80) cc_final: 0.7552 (m-80) REVERT: E 49 ARG cc_start: 0.8485 (ptm160) cc_final: 0.8031 (ptp-170) REVERT: E 50 GLU cc_start: 0.8345 (pt0) cc_final: 0.7956 (pt0) REVERT: E 68 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7745 (pp30) REVERT: E 71 VAL cc_start: 0.9117 (t) cc_final: 0.8855 (t) REVERT: E 85 GLN cc_start: 0.7885 (mt0) cc_final: 0.7508 (mt0) REVERT: E 105 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7497 (tm-30) REVERT: E 113 HIS cc_start: 0.7669 (t70) cc_final: 0.7341 (t70) REVERT: E 117 VAL cc_start: 0.9160 (t) cc_final: 0.8866 (p) REVERT: E 119 ILE cc_start: 0.9042 (pt) cc_final: 0.8119 (pt) REVERT: E 120 MET cc_start: 0.6746 (mtt) cc_final: 0.6370 (mpp) REVERT: E 125 GLN cc_start: 0.8717 (mt0) cc_final: 0.8360 (mm-40) outliers start: 35 outliers final: 22 residues processed: 417 average time/residue: 0.3446 time to fit residues: 186.1380 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 : 0.909 ------------------------------------------------------------------------------- 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: 0.7980 chunk 46 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 K 78 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3994 r_free = 0.3994 target = 0.140738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096317 restraints weight = 29054.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.099519 restraints weight = 15838.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.101536 restraints weight = 10888.477| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13814 Z= 0.209 Angle : 0.690 13.215 19943 Z= 0.391 Chirality : 0.037 0.198 2253 Planarity : 0.006 0.063 1485 Dihedral : 29.624 152.348 4242 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: -0.85 (0.27), residues: 831 helix: -0.07 (0.22), residues: 535 sheet: -4.15 (1.20), residues: 10 loop : -1.21 (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 0.014 0.002 PHE A 84 TYR 0.022 0.002 TYR F 51 ARG 0.009 0.001 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.05940 ( 658) hydrogen bonds : angle 3.34646 ( 1637) covalent geometry : bond 0.00471 (13814) covalent geometry : angle 0.69046 (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 445 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 397 time to evaluate : 1.055 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: 0.9066 (m110) cc_final: 0.8668 (m-40) REVERT: B 35 ARG cc_start: 0.9282 (mtp85) cc_final: 0.8945 (mtp85) REVERT: B 39 ARG cc_start: 0.9242 (mmt-90) cc_final: 0.8883 (tpp80) REVERT: B 45 ARG cc_start: 0.9047 (mtp-110) cc_final: 0.8738 (ttp80) REVERT: B 63 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 79 LYS cc_start: 0.9074 (mmtp) cc_final: 0.8783 (mmmm) REVERT: C 32 ARG cc_start: 0.7956 (ttp80) cc_final: 0.6888 (ttt180) REVERT: C 71 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7549 (ttp-110) REVERT: C 89 ASN cc_start: 0.8635 (m110) cc_final: 0.8362 (m-40) REVERT: C 95 LYS cc_start: 0.9147 (pttt) cc_final: 0.8829 (ptpp) REVERT: C 110 ASN cc_start: 0.9039 (t0) cc_final: 0.8646 (t0) REVERT: C 115 LEU cc_start: 0.9020 (mt) cc_final: 0.8686 (mm) REVERT: C 116 LEU cc_start: 0.8944 (tp) cc_final: 0.8526 (mp) REVERT: D 49 THR cc_start: 0.8492 (m) cc_final: 0.8148 (p) REVERT: D 59 MET cc_start: 0.9697 (mmm) cc_final: 0.9441 (tpp) REVERT: D 64 ASN cc_start: 0.8826 (m110) cc_final: 0.8451 (m110) REVERT: D 65 ASP cc_start: 0.8771 (t70) cc_final: 0.8551 (t70) REVERT: D 83 ARG cc_start: 0.8077 (mmt90) cc_final: 0.7857 (mmt90) REVERT: D 92 GLN cc_start: 0.8352 (pt0) cc_final: 0.7805 (pp30) REVERT: D 102 GLU cc_start: 0.7982 (tp30) cc_final: 0.7595 (tp30) REVERT: D 105 LYS cc_start: 0.8794 (tptp) cc_final: 0.8287 (tptp) REVERT: D 109 SER cc_start: 0.9429 (t) cc_final: 0.8849 (p) REVERT: D 110 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7933 (mt-10) REVERT: D 113 LYS cc_start: 0.8974 (mmtm) cc_final: 0.8774 (mmtm) REVERT: D 117 LYS cc_start: 0.9320 (ttpt) cc_final: 0.9081 (pttp) REVERT: F 25 ASN cc_start: 0.8656 (m-40) cc_final: 0.8237 (m-40) REVERT: F 39 ARG cc_start: 0.9291 (mmt-90) cc_final: 0.9035 (mmt-90) REVERT: F 44 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8480 (mtmm) REVERT: F 45 ARG cc_start: 0.9130 (mtp180) cc_final: 0.7986 (mmm-85) REVERT: F 53 GLU cc_start: 0.8566 (tp30) cc_final: 0.8038 (tp30) REVERT: F 63 GLU cc_start: 0.7996 (pt0) cc_final: 0.7696 (pp20) REVERT: F 88 TYR cc_start: 0.9347 (m-10) cc_final: 0.8845 (m-80) REVERT: G 39 TYR cc_start: 0.9114 (m-80) cc_final: 0.8533 (m-80) REVERT: G 42 ARG cc_start: 0.8451 (mtp-110) cc_final: 0.8067 (mtm-85) REVERT: G 58 LEU cc_start: 0.8568 (mt) cc_final: 0.8240 (mp) REVERT: G 61 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8300 (mm-30) REVERT: G 64 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7648 (tm-30) REVERT: G 68 ASN cc_start: 0.8446 (p0) cc_final: 0.7978 (p0) REVERT: G 72 ASP cc_start: 0.7833 (m-30) cc_final: 0.7588 (m-30) REVERT: G 78 ILE cc_start: 0.8805 (mt) cc_final: 0.8453 (mt) REVERT: G 81 ARG cc_start: 0.8766 (tpt90) cc_final: 0.8559 (tpt90) REVERT: G 95 LYS cc_start: 0.9144 (pttp) cc_final: 0.8489 (ptpp) REVERT: H 34 TYR cc_start: 0.8294 (m-80) cc_final: 0.7858 (m-10) REVERT: H 40 LYS cc_start: 0.9497 (tppt) cc_final: 0.8847 (tppt) REVERT: H 43 LYS cc_start: 0.8559 (pptt) cc_final: 0.8235 (pptt) REVERT: H 44 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8493 (mm110) REVERT: H 56 MET cc_start: 0.8069 (tmm) cc_final: 0.7851 (tmm) REVERT: H 59 MET cc_start: 0.9232 (mmp) cc_final: 0.8973 (mmp) REVERT: H 102 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8039 (mm-30) REVERT: H 105 LYS cc_start: 0.9232 (ptmm) cc_final: 0.8708 (pttm) REVERT: K 40 LEU cc_start: 0.4782 (OUTLIER) cc_final: 0.4458 (tp) REVERT: A 74 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9123 (tp) REVERT: A 76 GLN cc_start: 0.8692 (mm110) cc_final: 0.8437 (mm-40) REVERT: A 79 LYS cc_start: 0.9120 (tptp) cc_final: 0.8763 (tptt) REVERT: A 83 ARG cc_start: 0.8086 (mmp80) cc_final: 0.7786 (mmp80) REVERT: A 90 MET cc_start: 0.9279 (mmm) cc_final: 0.9056 (mmm) REVERT: E 39 HIS cc_start: 0.7445 (p-80) cc_final: 0.6948 (p-80) REVERT: E 41 TYR cc_start: 0.8282 (m-80) cc_final: 0.8064 (m-80) REVERT: E 49 ARG cc_start: 0.8634 (ptm160) cc_final: 0.7987 (ptp90) REVERT: E 50 GLU cc_start: 0.8296 (pt0) cc_final: 0.7722 (pt0) REVERT: E 63 ARG cc_start: 0.7863 (mmp80) cc_final: 0.7622 (mmp80) REVERT: E 67 PHE cc_start: 0.8901 (t80) cc_final: 0.8137 (t80) REVERT: E 68 GLN cc_start: 0.8418 (tm-30) cc_final: 0.7981 (pp30) REVERT: E 73 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: E 85 GLN cc_start: 0.8487 (mt0) cc_final: 0.7727 (mt0) REVERT: E 105 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7450 (tm-30) REVERT: E 113 HIS cc_start: 0.7860 (t70) cc_final: 0.7531 (t70) REVERT: E 117 VAL cc_start: 0.9442 (t) cc_final: 0.9227 (p) REVERT: E 120 MET cc_start: 0.7410 (mtt) cc_final: 0.6756 (mpp) REVERT: E 125 GLN cc_start: 0.8686 (mt0) cc_final: 0.8475 (mm-40) outliers start: 48 outliers final: 31 residues processed: 414 average time/residue: 0.3433 time to fit residues: 183.9428 Evaluate side-chains 408 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 374 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 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: 0.5980 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN G 73 ASN G 112 GLN H 92 GLN A 85 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.141446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099223 restraints weight = 29649.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102419 restraints weight = 16021.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104454 restraints weight = 10956.412| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13814 Z= 0.171 Angle : 0.657 12.205 19943 Z= 0.373 Chirality : 0.036 0.206 2253 Planarity : 0.005 0.061 1485 Dihedral : 29.522 152.137 4239 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.75 % Allowed : 30.01 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.02 (0.28), residues: 831 helix: 0.65 (0.22), residues: 533 sheet: -3.82 (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 0.005 0.001 HIS E 113 PHE 0.029 0.002 PHE A 67 TYR 0.018 0.002 TYR D 37 ARG 0.009 0.001 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.05235 ( 658) hydrogen bonds : angle 3.18349 ( 1637) covalent geometry : bond 0.00384 (13814) covalent geometry : angle 0.65694 (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 438 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 397 time to evaluate : 1.028 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 25 ASN cc_start: 0.8815 (m110) cc_final: 0.8401 (m-40) REVERT: B 45 ARG cc_start: 0.9102 (mtp-110) cc_final: 0.8827 (mtp85) REVERT: B 55 ARG cc_start: 0.8573 (mtt90) cc_final: 0.8250 (ttm110) REVERT: B 63 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 79 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8843 (mmmm) REVERT: C 17 ARG cc_start: 0.8954 (mtm180) cc_final: 0.8482 (mtt90) REVERT: C 24 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8096 (mm-40) REVERT: C 29 ARG cc_start: 0.8579 (tpp80) cc_final: 0.6497 (tpp80) REVERT: C 32 ARG cc_start: 0.7726 (ttp80) cc_final: 0.6947 (ttp-170) REVERT: C 35 ARG cc_start: 0.8439 (tmm160) cc_final: 0.8163 (ttp80) REVERT: C 64 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8479 (tm-30) REVERT: C 71 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7673 (ttp-110) REVERT: C 75 LYS cc_start: 0.9285 (mmtm) cc_final: 0.8950 (mmmm) REVERT: C 89 ASN cc_start: 0.8584 (m110) cc_final: 0.8206 (m-40) REVERT: C 92 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7815 (mm-30) REVERT: C 95 LYS cc_start: 0.8980 (pttt) cc_final: 0.8630 (pttp) REVERT: C 110 ASN cc_start: 0.9057 (t0) cc_final: 0.8736 (t0) REVERT: C 115 LEU cc_start: 0.8946 (mt) cc_final: 0.8721 (mt) REVERT: C 116 LEU cc_start: 0.9002 (tp) cc_final: 0.8717 (mt) REVERT: D 31 LYS cc_start: 0.8485 (mppt) cc_final: 0.8278 (mppt) REVERT: D 36 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8998 (pt) REVERT: D 49 THR cc_start: 0.8730 (m) cc_final: 0.8331 (p) REVERT: D 59 MET cc_start: 0.9624 (mmm) cc_final: 0.9421 (tpp) REVERT: D 73 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8990 (mm-30) REVERT: D 92 GLN cc_start: 0.8175 (pt0) cc_final: 0.7663 (pp30) REVERT: D 102 GLU cc_start: 0.7923 (tp30) cc_final: 0.7493 (tp30) REVERT: D 105 LYS cc_start: 0.8799 (tptp) cc_final: 0.8377 (tptp) REVERT: D 109 SER cc_start: 0.9439 (t) cc_final: 0.8857 (p) REVERT: D 110 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8130 (mt-10) REVERT: D 113 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8652 (mmtm) REVERT: D 117 LYS cc_start: 0.9242 (ttpt) cc_final: 0.8985 (pttp) REVERT: F 25 ASN cc_start: 0.8641 (m-40) cc_final: 0.8419 (m-40) REVERT: F 53 GLU cc_start: 0.8448 (tp30) cc_final: 0.7953 (tp30) REVERT: F 70 VAL cc_start: 0.9297 (t) cc_final: 0.9091 (p) REVERT: F 88 TYR cc_start: 0.9302 (m-10) cc_final: 0.8815 (m-80) REVERT: G 39 TYR cc_start: 0.9150 (m-80) cc_final: 0.8945 (m-80) REVERT: G 61 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8042 (mm-30) REVERT: G 64 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7485 (tm-30) REVERT: G 68 ASN cc_start: 0.8373 (p0) cc_final: 0.7891 (p0) REVERT: G 78 ILE cc_start: 0.8854 (mt) cc_final: 0.8518 (mt) REVERT: G 84 GLN cc_start: 0.9404 (tp-100) cc_final: 0.9195 (tp-100) REVERT: G 95 LYS cc_start: 0.9167 (pttp) cc_final: 0.8943 (pttm) REVERT: H 31 LYS cc_start: 0.8606 (mppt) cc_final: 0.8396 (mppt) REVERT: H 40 LYS cc_start: 0.9359 (tppt) cc_final: 0.8892 (tppt) REVERT: H 43 LYS cc_start: 0.8617 (pptt) cc_final: 0.8249 (pptt) REVERT: H 44 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8281 (mm-40) REVERT: H 48 ASP cc_start: 0.8463 (m-30) cc_final: 0.8252 (p0) REVERT: H 56 MET cc_start: 0.7998 (tmm) cc_final: 0.7711 (tmm) REVERT: H 73 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.7696 (mm-30) REVERT: H 102 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8767 (mm-30) REVERT: A 76 GLN cc_start: 0.8759 (mm110) cc_final: 0.8508 (mm-40) REVERT: A 79 LYS cc_start: 0.9141 (tptp) cc_final: 0.8720 (tptp) REVERT: E 39 HIS cc_start: 0.7363 (p-80) cc_final: 0.7040 (p-80) REVERT: E 60 LEU cc_start: 0.8871 (mm) cc_final: 0.7973 (mm) REVERT: E 68 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7891 (pp30) REVERT: E 73 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7917 (tp30) REVERT: E 78 PHE cc_start: 0.8670 (m-80) cc_final: 0.8454 (m-10) REVERT: E 85 GLN cc_start: 0.8422 (mt0) cc_final: 0.8205 (mt0) REVERT: E 90 MET cc_start: 0.9325 (mmp) cc_final: 0.9075 (mmp) REVERT: E 93 GLN cc_start: 0.7890 (tm-30) cc_final: 0.6580 (tm-30) REVERT: E 94 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8430 (mt-10) REVERT: E 97 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8547 (mt-10) REVERT: E 105 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7535 (tm-30) REVERT: E 113 HIS cc_start: 0.8174 (t70) cc_final: 0.7731 (t-90) REVERT: E 115 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8571 (mmmm) REVERT: E 117 VAL cc_start: 0.9443 (t) cc_final: 0.9180 (p) REVERT: E 120 MET cc_start: 0.7442 (mtt) cc_final: 0.6999 (mpp) outliers start: 41 outliers final: 27 residues processed: 407 average time/residue: 0.3433 time to fit residues: 180.7837 Evaluate side-chains 412 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 382 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 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 36 ILE Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 38 VAL 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 93 THR Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain A residue 46 VAL 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 71 VAL 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: 0.6980 chunk 88 optimal weight: 50.0000 chunk 35 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 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** D 64 ASN G 73 ASN G 89 ASN H 64 ASN A 108 ASN A 125 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 = 0.4024 r_free = 0.4024 target = 0.140417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097905 restraints weight = 30021.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.101078 restraints weight = 16326.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.103140 restraints weight = 11202.188| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13814 Z= 0.173 Angle : 0.646 13.771 19943 Z= 0.366 Chirality : 0.036 0.202 2253 Planarity : 0.005 0.061 1485 Dihedral : 29.492 150.154 4237 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.05 % Allowed : 31.98 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.29), residues: 831 helix: 1.05 (0.23), residues: 529 sheet: -3.67 (1.46), residues: 10 loop : -0.80 (0.34), residues: 292 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 0.028 0.002 PHE B 61 TYR 0.017 0.002 TYR A 99 ARG 0.010 0.001 ARG G 81 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 658) hydrogen bonds : angle 3.14222 ( 1637) covalent geometry : bond 0.00386 (13814) covalent geometry : angle 0.64566 (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 426 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 390 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.9360 (tptp) cc_final: 0.8831 (tppp) REVERT: B 44 LYS cc_start: 0.9251 (tttt) cc_final: 0.9019 (mtmt) REVERT: B 45 ARG cc_start: 0.9085 (mtp-110) cc_final: 0.8768 (mtp85) REVERT: B 51 TYR cc_start: 0.7383 (m-80) cc_final: 0.6610 (m-80) REVERT: B 55 ARG cc_start: 0.8627 (mtt90) cc_final: 0.8335 (ttm110) REVERT: B 63 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7748 (mt-10) REVERT: B 73 THR cc_start: 0.9406 (t) cc_final: 0.9154 (t) REVERT: B 79 LYS cc_start: 0.9198 (mmtp) cc_final: 0.8671 (mmmm) REVERT: C 17 ARG cc_start: 0.8947 (mtm180) cc_final: 0.8444 (mtp180) REVERT: C 24 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8138 (mm110) REVERT: C 29 ARG cc_start: 0.8191 (tpp80) cc_final: 0.6800 (tpp80) REVERT: C 32 ARG cc_start: 0.8054 (ttp80) cc_final: 0.6916 (ttp80) REVERT: C 36 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7395 (pttm) REVERT: C 64 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8446 (tm-30) REVERT: C 71 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7753 (ttp-110) REVERT: C 84 GLN cc_start: 0.9288 (tp-100) cc_final: 0.9045 (tp-100) REVERT: C 89 ASN cc_start: 0.8579 (m110) cc_final: 0.8187 (m110) REVERT: C 95 LYS cc_start: 0.8865 (pttt) cc_final: 0.8531 (pttm) REVERT: C 110 ASN cc_start: 0.9173 (t0) cc_final: 0.8908 (t0) REVERT: C 115 LEU cc_start: 0.8952 (mt) cc_final: 0.8465 (mt) REVERT: C 116 LEU cc_start: 0.9040 (tp) cc_final: 0.8738 (mt) REVERT: D 39 TYR cc_start: 0.8202 (t80) cc_final: 0.7628 (t80) REVERT: D 64 ASN cc_start: 0.8604 (m-40) cc_final: 0.8063 (m110) REVERT: D 73 GLU cc_start: 0.9162 (mm-30) cc_final: 0.7970 (mm-30) REVERT: D 83 ARG cc_start: 0.8082 (mmt90) cc_final: 0.7761 (mmt90) REVERT: D 92 GLN cc_start: 0.8561 (pt0) cc_final: 0.7951 (pp30) REVERT: D 102 GLU cc_start: 0.7940 (tp30) cc_final: 0.7529 (tp30) REVERT: D 105 LYS cc_start: 0.8786 (tptp) cc_final: 0.8337 (tptp) REVERT: D 109 SER cc_start: 0.9398 (t) cc_final: 0.8837 (p) REVERT: D 110 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8103 (mt-10) REVERT: D 113 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8598 (mmtm) REVERT: D 117 LYS cc_start: 0.9259 (ttpt) cc_final: 0.8934 (ptmt) REVERT: F 39 ARG cc_start: 0.8965 (mmt-90) cc_final: 0.8764 (mmt180) REVERT: F 44 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8213 (mtmm) REVERT: F 74 GLU cc_start: 0.8387 (tp30) cc_final: 0.8172 (tp30) REVERT: F 78 ARG cc_start: 0.8549 (tpp80) cc_final: 0.7713 (tpp80) REVERT: F 88 TYR cc_start: 0.9317 (m-10) cc_final: 0.8772 (m-80) REVERT: F 90 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9208 (mp) REVERT: G 39 TYR cc_start: 0.9117 (m-80) cc_final: 0.8816 (m-80) REVERT: G 42 ARG cc_start: 0.8587 (mtm110) cc_final: 0.7690 (mtm180) REVERT: G 61 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8095 (mm-30) REVERT: G 64 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7467 (tm-30) REVERT: G 68 ASN cc_start: 0.8392 (p0) cc_final: 0.7826 (p0) REVERT: G 78 ILE cc_start: 0.8957 (mt) cc_final: 0.8658 (mm) REVERT: G 81 ARG cc_start: 0.8560 (tpt90) cc_final: 0.8195 (tpt90) REVERT: G 92 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8058 (mm-30) REVERT: G 95 LYS cc_start: 0.9070 (pttp) cc_final: 0.8743 (pttm) REVERT: H 40 LYS cc_start: 0.9360 (tppt) cc_final: 0.8866 (tppt) REVERT: H 43 LYS cc_start: 0.8595 (pptt) cc_final: 0.8362 (pptt) REVERT: H 44 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8272 (mm-40) REVERT: H 48 ASP cc_start: 0.8437 (m-30) cc_final: 0.8103 (p0) REVERT: H 113 LYS cc_start: 0.9296 (mtmt) cc_final: 0.8970 (ptpt) REVERT: H 117 LYS cc_start: 0.9062 (tppt) cc_final: 0.8609 (tptp) REVERT: A 76 GLN cc_start: 0.8761 (mm110) cc_final: 0.8523 (mm-40) REVERT: A 79 LYS cc_start: 0.9177 (tptp) cc_final: 0.8817 (tptp) REVERT: E 39 HIS cc_start: 0.7427 (p-80) cc_final: 0.7176 (p-80) REVERT: E 53 ARG cc_start: 0.8881 (tpt90) cc_final: 0.7761 (tmt-80) REVERT: E 60 LEU cc_start: 0.8934 (mm) cc_final: 0.8114 (mm) REVERT: E 67 PHE cc_start: 0.8899 (t80) cc_final: 0.8240 (t80) REVERT: E 68 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7992 (pp30) REVERT: E 73 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: E 76 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8752 (tm-30) REVERT: E 81 ASP cc_start: 0.8390 (m-30) cc_final: 0.8101 (m-30) REVERT: E 85 GLN cc_start: 0.8503 (mt0) cc_final: 0.8269 (mt0) REVERT: E 87 SER cc_start: 0.9219 (m) cc_final: 0.8992 (p) REVERT: E 90 MET cc_start: 0.9339 (mmp) cc_final: 0.9088 (mmp) REVERT: E 93 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7761 (tm-30) REVERT: E 94 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8454 (mt-10) REVERT: E 97 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8287 (mt-10) REVERT: E 105 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7519 (tm-30) REVERT: E 115 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8536 (mmmm) REVERT: E 117 VAL cc_start: 0.9476 (t) cc_final: 0.9218 (p) REVERT: E 125 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8354 (mp10) outliers start: 36 outliers final: 27 residues processed: 402 average time/residue: 0.3454 time to fit residues: 180.0543 Evaluate side-chains 405 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 376 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 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 63 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 42 LEU 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 62 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 57 SER 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: 0.5980 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN G 73 ASN G 89 ASN G 112 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4018 r_free = 0.4018 target = 0.139773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097166 restraints weight = 30571.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100338 restraints weight = 16601.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102358 restraints weight = 11401.919| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13814 Z= 0.176 Angle : 0.654 13.765 19943 Z= 0.368 Chirality : 0.036 0.206 2253 Planarity : 0.005 0.060 1485 Dihedral : 29.537 149.861 4237 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.19 % Allowed : 35.06 % Favored : 59.75 % 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 (0.29), residues: 831 helix: 1.15 (0.23), residues: 529 sheet: -3.49 (1.49), residues: 10 loop : -0.64 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.004 0.001 HIS E 113 PHE 0.027 0.002 PHE A 67 TYR 0.019 0.001 TYR H 37 ARG 0.012 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.05024 ( 658) hydrogen bonds : angle 3.16329 ( 1637) covalent geometry : bond 0.00399 (13814) covalent geometry : angle 0.65407 (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: 37 poor density : 390 time to evaluate : 1.033 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 24 ASP cc_start: 0.8230 (p0) cc_final: 0.8024 (p0) REVERT: B 31 LYS cc_start: 0.9378 (tptp) cc_final: 0.9055 (tptp) REVERT: B 32 PRO cc_start: 0.9224 (Cg_exo) cc_final: 0.8976 (Cg_endo) REVERT: B 39 ARG cc_start: 0.9125 (tpp-160) cc_final: 0.8746 (mmt90) REVERT: B 45 ARG cc_start: 0.9081 (mtp-110) cc_final: 0.8795 (mtp85) REVERT: B 51 TYR cc_start: 0.7657 (m-80) cc_final: 0.7394 (m-80) REVERT: B 55 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8349 (ttm110) REVERT: B 63 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7810 (mt-10) REVERT: B 79 LYS cc_start: 0.9193 (mmtp) cc_final: 0.8567 (mmmm) REVERT: B 88 TYR cc_start: 0.8831 (m-10) cc_final: 0.7844 (m-10) REVERT: C 24 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8022 (mm110) REVERT: C 29 ARG cc_start: 0.8135 (tpp80) cc_final: 0.6479 (tpp80) REVERT: C 32 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7302 (tmm-80) REVERT: C 71 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7800 (ttp-110) REVERT: C 75 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8780 (mmmm) REVERT: C 89 ASN cc_start: 0.8572 (m110) cc_final: 0.8219 (m110) REVERT: C 110 ASN cc_start: 0.9193 (t0) cc_final: 0.8957 (t0) REVERT: C 115 LEU cc_start: 0.8982 (mt) cc_final: 0.8445 (tp) REVERT: C 116 LEU cc_start: 0.9104 (tp) cc_final: 0.8865 (mt) REVERT: D 31 LYS cc_start: 0.8564 (mppt) cc_final: 0.8147 (mmtm) REVERT: D 43 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8984 (tppt) REVERT: D 64 ASN cc_start: 0.8686 (m-40) cc_final: 0.8049 (m-40) REVERT: D 73 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8693 (mm-30) REVERT: D 83 ARG cc_start: 0.8148 (mmt90) cc_final: 0.7803 (mmt90) REVERT: D 92 GLN cc_start: 0.8458 (pt0) cc_final: 0.7670 (pp30) REVERT: D 105 LYS cc_start: 0.8810 (tptp) cc_final: 0.8457 (tptp) REVERT: D 109 SER cc_start: 0.9408 (t) cc_final: 0.8807 (p) REVERT: D 113 LYS cc_start: 0.8899 (mmtm) cc_final: 0.8553 (mmtm) REVERT: D 117 LYS cc_start: 0.9280 (ttpt) cc_final: 0.8950 (ptmt) REVERT: F 39 ARG cc_start: 0.9063 (mmt-90) cc_final: 0.8756 (mmt180) REVERT: F 44 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8271 (mtmm) REVERT: F 61 PHE cc_start: 0.8818 (t80) cc_final: 0.8603 (t80) REVERT: F 63 GLU cc_start: 0.7684 (pp20) cc_final: 0.7436 (pp20) REVERT: F 64 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8530 (t0) REVERT: F 88 TYR cc_start: 0.9344 (m-10) cc_final: 0.8808 (m-80) REVERT: F 90 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9184 (mp) REVERT: G 17 ARG cc_start: 0.9071 (mtm180) cc_final: 0.7522 (ptp-170) REVERT: G 39 TYR cc_start: 0.9059 (m-80) cc_final: 0.8851 (m-80) REVERT: G 42 ARG cc_start: 0.8639 (mtm110) cc_final: 0.7699 (mtm180) REVERT: G 61 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8123 (mm-30) REVERT: G 64 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7441 (tm-30) REVERT: G 68 ASN cc_start: 0.8487 (p0) cc_final: 0.7894 (p0) REVERT: G 78 ILE cc_start: 0.9060 (mt) cc_final: 0.8651 (mm) REVERT: G 79 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8422 (mm) REVERT: G 81 ARG cc_start: 0.8543 (tpt90) cc_final: 0.8119 (tpt90) REVERT: H 32 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8017 (tp30) REVERT: H 40 LYS cc_start: 0.9329 (tppt) cc_final: 0.8879 (tppt) REVERT: H 43 LYS cc_start: 0.8611 (pptt) cc_final: 0.8319 (pptt) REVERT: H 44 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8122 (mm-40) REVERT: H 48 ASP cc_start: 0.8423 (m-30) cc_final: 0.8147 (p0) REVERT: H 89 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7500 (ptm-80) REVERT: H 113 LYS cc_start: 0.9268 (mtmt) cc_final: 0.9025 (tptt) REVERT: A 49 ARG cc_start: 0.8761 (mtp-110) cc_final: 0.8298 (mtp-110) REVERT: A 62 ILE cc_start: 0.8595 (mt) cc_final: 0.8364 (mp) REVERT: A 76 GLN cc_start: 0.8809 (mm110) cc_final: 0.8488 (mm-40) REVERT: A 79 LYS cc_start: 0.9194 (tptp) cc_final: 0.8856 (tptp) REVERT: E 39 HIS cc_start: 0.7637 (p-80) cc_final: 0.7325 (p-80) REVERT: E 53 ARG cc_start: 0.8879 (tpt90) cc_final: 0.7807 (tpt90) REVERT: E 60 LEU cc_start: 0.9075 (mm) cc_final: 0.7994 (mm) REVERT: E 67 PHE cc_start: 0.8947 (t80) cc_final: 0.8275 (t80) REVERT: E 73 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8150 (tp30) REVERT: E 76 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8755 (tm-30) REVERT: E 81 ASP cc_start: 0.8618 (m-30) cc_final: 0.8315 (m-30) REVERT: E 85 GLN cc_start: 0.8539 (mt0) cc_final: 0.8223 (mt0) REVERT: E 90 MET cc_start: 0.9357 (mmp) cc_final: 0.9103 (mmp) REVERT: E 93 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7335 (tm-30) REVERT: E 94 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8361 (mt-10) REVERT: E 97 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8235 (mt-10) REVERT: E 105 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7552 (tm-30) REVERT: E 115 LYS cc_start: 0.8978 (ttmm) cc_final: 0.8572 (mmmm) REVERT: E 117 VAL cc_start: 0.9480 (t) cc_final: 0.9247 (p) outliers start: 37 outliers final: 29 residues processed: 403 average time/residue: 0.3471 time to fit residues: 179.8722 Evaluate side-chains 413 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 379 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR 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 C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 64 ASN 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 79 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.0270 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.0050 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.3852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 89 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.141207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098094 restraints weight = 30620.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.101253 restraints weight = 16964.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103303 restraints weight = 11780.471| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13814 Z= 0.159 Angle : 0.663 15.712 19943 Z= 0.371 Chirality : 0.036 0.212 2253 Planarity : 0.005 0.061 1485 Dihedral : 29.517 149.153 4237 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.19 % Allowed : 36.47 % Favored : 58.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.28), residues: 831 helix: 1.26 (0.23), residues: 512 sheet: -3.40 (1.53), residues: 10 loop : -0.58 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.005 0.001 HIS D 106 PHE 0.016 0.001 PHE B 100 TYR 0.033 0.002 TYR C 57 ARG 0.012 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 658) hydrogen bonds : angle 3.20014 ( 1637) covalent geometry : bond 0.00358 (13814) covalent geometry : angle 0.66325 (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 433 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 396 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.9378 (tptp) cc_final: 0.9102 (tptp) REVERT: B 32 PRO cc_start: 0.9279 (Cg_exo) cc_final: 0.8995 (Cg_endo) REVERT: B 39 ARG cc_start: 0.9222 (tpp-160) cc_final: 0.8760 (mmt90) REVERT: B 55 ARG cc_start: 0.8657 (mtt90) cc_final: 0.8362 (ttm110) REVERT: B 63 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 79 LYS cc_start: 0.9042 (mmtp) cc_final: 0.8642 (mmmm) REVERT: C 17 ARG cc_start: 0.8924 (mtm180) cc_final: 0.8579 (mtt90) REVERT: C 24 GLN cc_start: 0.8812 (mm-40) cc_final: 0.7540 (mm-40) REVERT: C 25 PHE cc_start: 0.8874 (m-10) cc_final: 0.8587 (m-10) REVERT: C 32 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7709 (tmm-80) REVERT: C 34 LEU cc_start: 0.8619 (mt) cc_final: 0.8331 (mt) REVERT: C 35 ARG cc_start: 0.8649 (tpp80) cc_final: 0.7813 (tpp-160) REVERT: C 71 ARG cc_start: 0.8330 (ttm110) cc_final: 0.7848 (ttp-110) REVERT: C 75 LYS cc_start: 0.9082 (mmtm) cc_final: 0.8839 (mmmm) REVERT: C 84 GLN cc_start: 0.9332 (tp40) cc_final: 0.9127 (tp-100) REVERT: C 89 ASN cc_start: 0.8496 (m110) cc_final: 0.8120 (m110) REVERT: C 95 LYS cc_start: 0.8851 (pttp) cc_final: 0.8631 (pttm) REVERT: C 110 ASN cc_start: 0.9192 (t0) cc_final: 0.8958 (t0) REVERT: C 115 LEU cc_start: 0.8961 (mt) cc_final: 0.8449 (tp) REVERT: D 31 LYS cc_start: 0.8580 (mppt) cc_final: 0.8164 (mmtm) REVERT: D 64 ASN cc_start: 0.8877 (m-40) cc_final: 0.8334 (m-40) REVERT: D 92 GLN cc_start: 0.8451 (pt0) cc_final: 0.7656 (pp30) REVERT: D 105 LYS cc_start: 0.8655 (tptp) cc_final: 0.8241 (tptp) REVERT: D 106 HIS cc_start: 0.8113 (m-70) cc_final: 0.7868 (m170) REVERT: D 110 GLU cc_start: 0.8911 (tt0) cc_final: 0.8388 (mt-10) REVERT: D 117 LYS cc_start: 0.9275 (ttpt) cc_final: 0.8960 (ptmt) REVERT: F 44 LYS cc_start: 0.9017 (mtmm) cc_final: 0.8384 (mtmm) REVERT: F 61 PHE cc_start: 0.8921 (t80) cc_final: 0.8662 (t80) REVERT: F 63 GLU cc_start: 0.7705 (pp20) cc_final: 0.6729 (pp20) REVERT: F 88 TYR cc_start: 0.9288 (m-10) cc_final: 0.8805 (m-80) REVERT: F 90 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9190 (mp) REVERT: G 20 ARG cc_start: 0.8230 (mtm180) cc_final: 0.7793 (ptt180) REVERT: G 42 ARG cc_start: 0.8605 (mtm110) cc_final: 0.7988 (mtm180) REVERT: G 61 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8042 (mm-30) REVERT: G 64 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7539 (tm-30) REVERT: G 68 ASN cc_start: 0.8443 (p0) cc_final: 0.7646 (p0) REVERT: G 78 ILE cc_start: 0.8961 (mt) cc_final: 0.8455 (mm) REVERT: G 79 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8441 (mm) REVERT: G 81 ARG cc_start: 0.8608 (tpt90) cc_final: 0.8099 (tpt90) REVERT: G 112 GLN cc_start: 0.8478 (mm110) cc_final: 0.8149 (mm110) REVERT: H 32 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7733 (tp30) REVERT: H 40 LYS cc_start: 0.9348 (tppt) cc_final: 0.8873 (tppt) REVERT: H 43 LYS cc_start: 0.8444 (pptt) cc_final: 0.8173 (pptt) REVERT: H 44 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8056 (mm-40) REVERT: H 48 ASP cc_start: 0.8376 (m-30) cc_final: 0.8175 (p0) REVERT: H 89 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7483 (ptm-80) REVERT: H 92 GLN cc_start: 0.9309 (tt0) cc_final: 0.9006 (tt0) REVERT: H 113 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8980 (tptt) REVERT: H 117 LYS cc_start: 0.9073 (tppt) cc_final: 0.8562 (tptp) REVERT: A 49 ARG cc_start: 0.8727 (mtp-110) cc_final: 0.8313 (mtp-110) REVERT: A 56 LYS cc_start: 0.8676 (pttp) cc_final: 0.8304 (ptpp) REVERT: A 76 GLN cc_start: 0.8878 (mm110) cc_final: 0.8628 (mm-40) REVERT: A 79 LYS cc_start: 0.9213 (tptp) cc_final: 0.8865 (tptp) REVERT: A 106 ASP cc_start: 0.8333 (m-30) cc_final: 0.8097 (m-30) REVERT: E 39 HIS cc_start: 0.7633 (p-80) cc_final: 0.7309 (p-80) REVERT: E 52 ARG cc_start: 0.9088 (ttm110) cc_final: 0.8506 (ttm-80) REVERT: E 53 ARG cc_start: 0.8916 (tpt90) cc_final: 0.7843 (tpt90) REVERT: E 56 LYS cc_start: 0.8325 (mmtm) cc_final: 0.7895 (mptt) REVERT: E 60 LEU cc_start: 0.8937 (mm) cc_final: 0.7880 (mm) REVERT: E 67 PHE cc_start: 0.8935 (t80) cc_final: 0.8327 (t80) REVERT: E 68 GLN cc_start: 0.8269 (pp30) cc_final: 0.7940 (pp30) REVERT: E 73 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8128 (tp30) REVERT: E 76 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8723 (tm-30) REVERT: E 81 ASP cc_start: 0.8452 (m-30) cc_final: 0.8246 (m-30) REVERT: E 85 GLN cc_start: 0.8457 (mt0) cc_final: 0.8035 (mt0) REVERT: E 90 MET cc_start: 0.9354 (mmp) cc_final: 0.8990 (mmp) REVERT: E 93 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7294 (tm-30) REVERT: E 94 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8371 (mt-10) REVERT: E 97 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8211 (mt-10) REVERT: E 105 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7591 (tm-30) REVERT: E 115 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8507 (mmmm) REVERT: E 117 VAL cc_start: 0.9452 (t) cc_final: 0.9209 (p) REVERT: E 128 ARG cc_start: 0.8816 (mtp180) cc_final: 0.8507 (mtp-110) outliers start: 37 outliers final: 24 residues processed: 407 average time/residue: 0.3635 time to fit residues: 189.5670 Evaluate side-chains 410 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 382 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 73 ASN 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 D residue 77 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 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 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 65 LEU 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: 0.8980 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 106 HIS G 73 ASN H 64 ASN A 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.139409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096772 restraints weight = 30867.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099958 restraints weight = 16929.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102031 restraints weight = 11638.985| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.7149 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= 0.182 Angle : 0.689 15.622 19943 Z= 0.383 Chirality : 0.036 0.205 2253 Planarity : 0.005 0.062 1485 Dihedral : 29.559 148.556 4233 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.33 % Allowed : 37.31 % Favored : 57.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.23), residues: 526 sheet: -3.41 (1.45), residues: 10 loop : -0.46 (0.33), residues: 295 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 0.017 0.001 PHE B 100 TYR 0.035 0.002 TYR D 80 ARG 0.013 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.05060 ( 658) hydrogen bonds : angle 3.25695 ( 1637) covalent geometry : bond 0.00418 (13814) covalent geometry : angle 0.68862 (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 426 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 388 time to evaluate : 0.988 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 32 PRO cc_start: 0.9338 (Cg_exo) cc_final: 0.9124 (Cg_endo) REVERT: B 55 ARG cc_start: 0.8718 (mtt90) cc_final: 0.8400 (ttm110) REVERT: B 63 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7803 (mt-10) REVERT: B 79 LYS cc_start: 0.9085 (mmtp) cc_final: 0.8685 (mmmm) REVERT: C 24 GLN cc_start: 0.8581 (mm-40) cc_final: 0.7616 (mm110) REVERT: C 29 ARG cc_start: 0.8348 (tpp80) cc_final: 0.7938 (tpp80) REVERT: C 34 LEU cc_start: 0.8613 (mt) cc_final: 0.8322 (mt) REVERT: C 35 ARG cc_start: 0.8630 (tpp80) cc_final: 0.7843 (tpp-160) REVERT: C 56 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8783 (mm-30) REVERT: C 75 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8820 (mmmm) REVERT: C 84 GLN cc_start: 0.9335 (tp40) cc_final: 0.9135 (tp40) REVERT: C 95 LYS cc_start: 0.8831 (pttp) cc_final: 0.8489 (pttm) REVERT: C 108 LEU cc_start: 0.8793 (mt) cc_final: 0.8231 (tt) REVERT: C 115 LEU cc_start: 0.8946 (mt) cc_final: 0.8318 (tp) REVERT: C 116 LEU cc_start: 0.9082 (mt) cc_final: 0.8799 (mm) REVERT: D 31 LYS cc_start: 0.8627 (mppt) cc_final: 0.8184 (mmtm) REVERT: D 43 LYS cc_start: 0.9219 (mmmt) cc_final: 0.9006 (tppt) REVERT: D 64 ASN cc_start: 0.8912 (m-40) cc_final: 0.8376 (m110) REVERT: D 92 GLN cc_start: 0.8482 (pt0) cc_final: 0.7686 (pp30) REVERT: D 110 GLU cc_start: 0.8892 (tt0) cc_final: 0.8194 (mt-10) REVERT: D 117 LYS cc_start: 0.9255 (ttpt) cc_final: 0.9013 (tttt) REVERT: F 44 LYS cc_start: 0.9002 (mtmm) cc_final: 0.8288 (mtmm) REVERT: F 63 GLU cc_start: 0.7738 (pp20) cc_final: 0.6908 (pp20) REVERT: F 88 TYR cc_start: 0.9364 (m-10) cc_final: 0.8810 (m-80) REVERT: F 90 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9170 (mp) REVERT: G 17 ARG cc_start: 0.9001 (mtm180) cc_final: 0.8726 (mtt90) REVERT: G 20 ARG cc_start: 0.8350 (mtm180) cc_final: 0.7825 (ptt180) REVERT: G 35 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7803 (mmp80) REVERT: G 42 ARG cc_start: 0.8648 (mtm110) cc_final: 0.8042 (mtm180) REVERT: G 61 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8064 (mm-30) REVERT: G 68 ASN cc_start: 0.8463 (p0) cc_final: 0.7676 (p0) REVERT: G 78 ILE cc_start: 0.9001 (mt) cc_final: 0.8499 (mm) REVERT: G 79 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8480 (mm) REVERT: G 81 ARG cc_start: 0.8659 (tpt90) cc_final: 0.8259 (tpt90) REVERT: G 84 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8778 (tp-100) REVERT: G 89 ASN cc_start: 0.8461 (m-40) cc_final: 0.8185 (m-40) REVERT: G 112 GLN cc_start: 0.8373 (mm110) cc_final: 0.8164 (mm110) REVERT: H 29 THR cc_start: 0.8507 (t) cc_final: 0.8277 (m) REVERT: H 40 LYS cc_start: 0.9356 (tppt) cc_final: 0.8878 (tppt) REVERT: H 43 LYS cc_start: 0.8470 (pptt) cc_final: 0.8141 (pptt) REVERT: H 44 GLN cc_start: 0.8513 (mm-40) cc_final: 0.7935 (mm-40) REVERT: H 89 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7486 (ptm-80) REVERT: H 113 LYS cc_start: 0.9248 (mtmt) cc_final: 0.8924 (tptt) REVERT: H 117 LYS cc_start: 0.9240 (tppt) cc_final: 0.8580 (ttpp) REVERT: H 120 SER cc_start: 0.9418 (m) cc_final: 0.9075 (p) REVERT: A 49 ARG cc_start: 0.8750 (mtp-110) cc_final: 0.8483 (mtp180) REVERT: A 56 LYS cc_start: 0.8655 (pttp) cc_final: 0.8437 (pttm) REVERT: A 76 GLN cc_start: 0.8905 (mm110) cc_final: 0.8155 (mt0) REVERT: A 79 LYS cc_start: 0.9215 (tptp) cc_final: 0.8642 (tptp) REVERT: A 106 ASP cc_start: 0.8236 (m-30) cc_final: 0.7407 (m-30) REVERT: E 39 HIS cc_start: 0.7651 (p-80) cc_final: 0.7359 (p-80) REVERT: E 53 ARG cc_start: 0.8932 (tpt90) cc_final: 0.7808 (tpt90) REVERT: E 60 LEU cc_start: 0.8996 (mm) cc_final: 0.8071 (mp) REVERT: E 67 PHE cc_start: 0.8980 (t80) cc_final: 0.8168 (t80) REVERT: E 68 GLN cc_start: 0.8437 (pp30) cc_final: 0.8014 (pp30) REVERT: E 73 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8266 (tp30) REVERT: E 76 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8750 (tm-30) REVERT: E 85 GLN cc_start: 0.8609 (mt0) cc_final: 0.8398 (mt0) REVERT: E 90 MET cc_start: 0.9362 (mmp) cc_final: 0.9162 (mmp) REVERT: E 93 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7255 (tm-30) REVERT: E 94 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8385 (mt-10) REVERT: E 105 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7619 (tm-30) REVERT: E 115 LYS cc_start: 0.8870 (ttmm) cc_final: 0.8442 (mmmm) REVERT: E 117 VAL cc_start: 0.9480 (t) cc_final: 0.9255 (p) REVERT: E 128 ARG cc_start: 0.8811 (mtp180) cc_final: 0.8476 (mtp-110) outliers start: 38 outliers final: 30 residues processed: 398 average time/residue: 0.3563 time to fit residues: 182.9436 Evaluate side-chains 415 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 381 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 25 ASN 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 27 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 81 ASN 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 25 PHE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 79 ILE 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 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 65 LYS 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=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: 0.0770 chunk 69 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 overall best weight: 1.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 104 GLN D 81 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.137469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094272 restraints weight = 30789.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097316 restraints weight = 17376.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.099271 restraints weight = 12166.951| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.7461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13814 Z= 0.233 Angle : 0.736 16.849 19943 Z= 0.408 Chirality : 0.039 0.209 2253 Planarity : 0.005 0.061 1485 Dihedral : 29.660 148.307 4233 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.77 % Allowed : 39.27 % Favored : 55.96 % 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: 0.31 (0.28), residues: 831 helix: 0.74 (0.22), residues: 527 sheet: -3.34 (1.38), residues: 10 loop : -0.49 (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 0.019 0.002 PHE B 100 TYR 0.034 0.003 TYR D 80 ARG 0.010 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.05433 ( 658) hydrogen bonds : angle 3.49661 ( 1637) covalent geometry : bond 0.00533 (13814) covalent geometry : angle 0.73611 (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 415 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 381 time to evaluate : 0.979 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: 0.9421 (tppt) cc_final: 0.9064 (tppt) REVERT: B 32 PRO cc_start: 0.9446 (Cg_exo) cc_final: 0.9213 (Cg_endo) REVERT: B 39 ARG cc_start: 0.9117 (tpp-160) cc_final: 0.8330 (tpp-160) REVERT: B 63 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 79 LYS cc_start: 0.9081 (mmtp) cc_final: 0.8641 (mmmm) REVERT: C 20 ARG cc_start: 0.8927 (mmt-90) cc_final: 0.8670 (mmt-90) REVERT: C 24 GLN cc_start: 0.8625 (mm-40) cc_final: 0.7895 (mm110) REVERT: C 29 ARG cc_start: 0.8533 (tpp80) cc_final: 0.7720 (tpp80) REVERT: C 34 LEU cc_start: 0.8604 (mt) cc_final: 0.8323 (mt) REVERT: C 35 ARG cc_start: 0.8649 (tpp80) cc_final: 0.8167 (tpp-160) REVERT: C 56 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8651 (mm-30) REVERT: C 75 LYS cc_start: 0.9111 (mmtm) cc_final: 0.8779 (mmmm) REVERT: C 84 GLN cc_start: 0.9291 (tp40) cc_final: 0.9091 (tp40) REVERT: C 95 LYS cc_start: 0.8881 (pttp) cc_final: 0.8484 (pttm) REVERT: C 116 LEU cc_start: 0.9149 (mt) cc_final: 0.8935 (mm) REVERT: D 31 LYS cc_start: 0.8650 (mppt) cc_final: 0.8236 (mmtm) REVERT: D 39 TYR cc_start: 0.8343 (t80) cc_final: 0.7814 (t80) REVERT: D 43 LYS cc_start: 0.9237 (mmmt) cc_final: 0.9016 (tppt) REVERT: D 64 ASN cc_start: 0.8955 (m-40) cc_final: 0.8494 (m110) REVERT: D 92 GLN cc_start: 0.8466 (pt0) cc_final: 0.7709 (pp30) REVERT: D 110 GLU cc_start: 0.8896 (tt0) cc_final: 0.8297 (mt-10) REVERT: D 117 LYS cc_start: 0.9225 (ttpt) cc_final: 0.8943 (pttt) REVERT: F 88 TYR cc_start: 0.9423 (m-10) cc_final: 0.8801 (m-80) REVERT: F 90 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9147 (mp) REVERT: G 17 ARG cc_start: 0.9019 (mtm180) cc_final: 0.8762 (mtt90) REVERT: G 20 ARG cc_start: 0.8264 (mtm180) cc_final: 0.7820 (ptt180) REVERT: G 35 ARG cc_start: 0.8197 (tpp-160) cc_final: 0.7658 (mmm160) REVERT: G 38 ASN cc_start: 0.8839 (m-40) cc_final: 0.7776 (t0) REVERT: G 42 ARG cc_start: 0.8785 (mtm110) cc_final: 0.8199 (mtm180) REVERT: G 61 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8151 (mm-30) REVERT: G 68 ASN cc_start: 0.8482 (p0) cc_final: 0.8113 (p0) REVERT: G 78 ILE cc_start: 0.9064 (mt) cc_final: 0.8638 (mm) REVERT: G 81 ARG cc_start: 0.8584 (tpt90) cc_final: 0.8298 (tpt90) REVERT: G 84 GLN cc_start: 0.9203 (tp-100) cc_final: 0.8796 (tp-100) REVERT: G 89 ASN cc_start: 0.8665 (m-40) cc_final: 0.8244 (m110) REVERT: G 112 GLN cc_start: 0.8459 (mm110) cc_final: 0.8246 (mm110) REVERT: H 89 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7506 (ptm-80) REVERT: H 92 GLN cc_start: 0.9322 (tt0) cc_final: 0.9068 (tt0) REVERT: H 113 LYS cc_start: 0.9208 (mtmt) cc_final: 0.8931 (tptt) REVERT: H 117 LYS cc_start: 0.9324 (tppt) cc_final: 0.8787 (tptp) REVERT: A 42 ARG cc_start: 0.7756 (mmm-85) cc_final: 0.7295 (mmm160) REVERT: A 49 ARG cc_start: 0.8810 (mtp-110) cc_final: 0.8556 (mtp180) REVERT: A 56 LYS cc_start: 0.8669 (pttp) cc_final: 0.8455 (pttm) REVERT: A 79 LYS cc_start: 0.9074 (tptp) cc_final: 0.8813 (tptp) REVERT: E 39 HIS cc_start: 0.7666 (p-80) cc_final: 0.7443 (p-80) REVERT: E 52 ARG cc_start: 0.9282 (ttm-80) cc_final: 0.9058 (ttm-80) REVERT: E 53 ARG cc_start: 0.8965 (tpt90) cc_final: 0.7888 (tpt90) REVERT: E 56 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8228 (mmtm) REVERT: E 63 ARG cc_start: 0.7880 (mmp80) cc_final: 0.7377 (mmp80) REVERT: E 68 GLN cc_start: 0.8465 (pp30) cc_final: 0.7982 (pp30) REVERT: E 76 GLN cc_start: 0.9366 (tm-30) cc_final: 0.8786 (tm-30) REVERT: E 90 MET cc_start: 0.9222 (mmp) cc_final: 0.8846 (mmp) REVERT: E 93 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7970 (tm-30) REVERT: E 99 TYR cc_start: 0.9034 (t80) cc_final: 0.8808 (t80) REVERT: E 105 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7635 (tm-30) REVERT: E 115 LYS cc_start: 0.8966 (ttmm) cc_final: 0.8563 (mmmm) REVERT: E 117 VAL cc_start: 0.9339 (t) cc_final: 0.9093 (p) REVERT: E 128 ARG cc_start: 0.8888 (mtp180) cc_final: 0.8644 (mtp-110) outliers start: 34 outliers final: 28 residues processed: 391 average time/residue: 0.3503 time to fit residues: 176.0447 Evaluate side-chains 399 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 369 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 25 ASN 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 27 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL 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 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 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain 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 73 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 2 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 84 GLN D 81 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.139257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096780 restraints weight = 30900.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.099958 restraints weight = 17271.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.101976 restraints weight = 11949.350| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.7693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13814 Z= 0.184 Angle : 0.739 17.030 19943 Z= 0.406 Chirality : 0.037 0.216 2253 Planarity : 0.005 0.061 1485 Dihedral : 29.660 148.199 4233 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.21 % Allowed : 41.65 % Favored : 54.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.38 (0.28), residues: 831 helix: 0.89 (0.22), residues: 511 sheet: -3.36 (1.36), residues: 10 loop : -0.58 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.005 0.001 HIS E 113 PHE 0.011 0.001 PHE G 25 TYR 0.061 0.003 TYR D 80 ARG 0.013 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.05108 ( 658) hydrogen bonds : angle 3.39644 ( 1637) covalent geometry : bond 0.00426 (13814) covalent geometry : angle 0.73872 (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 413 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 383 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: B 31 LYS cc_start: 0.9397 (tppt) cc_final: 0.8806 (tppt) REVERT: B 63 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7839 (mt-10) REVERT: B 79 LYS cc_start: 0.9093 (mmtp) cc_final: 0.8662 (mmmm) REVERT: C 20 ARG cc_start: 0.8961 (mmt-90) cc_final: 0.8706 (mmt-90) REVERT: C 24 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7760 (mm110) REVERT: C 29 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7304 (tpp-160) REVERT: C 34 LEU cc_start: 0.8590 (mt) cc_final: 0.8263 (mt) REVERT: C 35 ARG cc_start: 0.8603 (tpp80) cc_final: 0.8231 (tpp-160) REVERT: C 56 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8886 (mm-30) REVERT: C 75 LYS cc_start: 0.9127 (mmtm) cc_final: 0.8866 (mmmm) REVERT: C 89 ASN cc_start: 0.8661 (m-40) cc_final: 0.8405 (m110) REVERT: C 95 LYS cc_start: 0.8851 (pttp) cc_final: 0.8488 (pttm) REVERT: C 116 LEU cc_start: 0.8980 (mt) cc_final: 0.8730 (mm) REVERT: D 31 LYS cc_start: 0.8797 (mppt) cc_final: 0.8390 (mmtm) REVERT: D 39 TYR cc_start: 0.8185 (t80) cc_final: 0.7707 (t80) REVERT: D 64 ASN cc_start: 0.8917 (m-40) cc_final: 0.8449 (m110) REVERT: D 73 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8307 (mm-30) REVERT: D 92 GLN cc_start: 0.8432 (pt0) cc_final: 0.7657 (pp30) REVERT: D 110 GLU cc_start: 0.8881 (tt0) cc_final: 0.8260 (mt-10) REVERT: D 113 LYS cc_start: 0.8867 (mttt) cc_final: 0.8619 (mttm) REVERT: D 117 LYS cc_start: 0.9228 (ttpt) cc_final: 0.8949 (pttt) REVERT: F 88 TYR cc_start: 0.9340 (m-10) cc_final: 0.8825 (m-80) REVERT: F 90 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9176 (mp) REVERT: G 17 ARG cc_start: 0.9065 (mtm180) cc_final: 0.8827 (mtt90) REVERT: G 20 ARG cc_start: 0.8315 (mtm180) cc_final: 0.7749 (ptt-90) REVERT: G 35 ARG cc_start: 0.8100 (tpp-160) cc_final: 0.7507 (mmm160) REVERT: G 38 ASN cc_start: 0.8781 (m-40) cc_final: 0.7753 (t0) REVERT: G 42 ARG cc_start: 0.8500 (mtm110) cc_final: 0.8050 (mtm180) REVERT: G 61 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8145 (mm-30) REVERT: G 68 ASN cc_start: 0.8471 (p0) cc_final: 0.8158 (p0) REVERT: G 78 ILE cc_start: 0.9069 (mt) cc_final: 0.8654 (mm) REVERT: G 81 ARG cc_start: 0.8714 (tpt90) cc_final: 0.8311 (tpt90) REVERT: G 84 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8655 (tp-100) REVERT: G 89 ASN cc_start: 0.8661 (m-40) cc_final: 0.8382 (m110) REVERT: G 92 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7975 (mm-30) REVERT: H 89 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7286 (ptm-80) REVERT: H 92 GLN cc_start: 0.9305 (tt0) cc_final: 0.9013 (tt0) REVERT: H 113 LYS cc_start: 0.9140 (mtmt) cc_final: 0.8855 (tptt) REVERT: H 117 LYS cc_start: 0.9323 (tppt) cc_final: 0.8815 (tptp) REVERT: A 41 TYR cc_start: 0.9127 (m-80) cc_final: 0.8766 (m-80) REVERT: A 42 ARG cc_start: 0.7750 (mmm-85) cc_final: 0.7291 (mmm160) REVERT: A 49 ARG cc_start: 0.8871 (mtp-110) cc_final: 0.8142 (ttt180) REVERT: A 56 LYS cc_start: 0.8686 (pttp) cc_final: 0.8472 (pttm) REVERT: A 76 GLN cc_start: 0.8638 (mm-40) cc_final: 0.7937 (mt0) REVERT: E 52 ARG cc_start: 0.9275 (ttm-80) cc_final: 0.9062 (ttm-80) REVERT: E 53 ARG cc_start: 0.8983 (tpt90) cc_final: 0.7932 (tpt90) REVERT: E 56 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8274 (mmtm) REVERT: E 63 ARG cc_start: 0.7649 (mmp80) cc_final: 0.7369 (mmp80) REVERT: E 68 GLN cc_start: 0.8411 (pp30) cc_final: 0.7896 (pp30) REVERT: E 76 GLN cc_start: 0.9334 (tm-30) cc_final: 0.8846 (tm-30) REVERT: E 85 GLN cc_start: 0.8694 (mt0) cc_final: 0.8152 (pt0) REVERT: E 90 MET cc_start: 0.9188 (mmp) cc_final: 0.8858 (mmp) REVERT: E 94 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8070 (mt-10) REVERT: E 99 TYR cc_start: 0.9006 (t80) cc_final: 0.8771 (t80) REVERT: E 105 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7542 (tm-30) REVERT: E 115 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8543 (mmmm) REVERT: E 117 VAL cc_start: 0.9359 (t) cc_final: 0.9131 (p) REVERT: E 129 ARG cc_start: 0.9029 (mmm160) cc_final: 0.8624 (ttp80) outliers start: 30 outliers final: 22 residues processed: 392 average time/residue: 0.3528 time to fit residues: 178.3597 Evaluate side-chains 402 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 378 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL 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 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 GLU Rotamers are restrained with sigma=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: 0.5980 chunk 6 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 51 optimal weight: 0.0770 chunk 21 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 89 ASN ** G 73 ASN ** 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 = 0.4023 r_free = 0.4023 target = 0.140085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.097171 restraints weight = 31447.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.100340 restraints weight = 17832.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102359 restraints weight = 12426.847| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.7880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13814 Z= 0.182 Angle : 0.740 18.140 19943 Z= 0.406 Chirality : 0.037 0.218 2253 Planarity : 0.005 0.060 1485 Dihedral : 29.644 147.621 4233 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.79 % Allowed : 41.51 % Favored : 54.70 % 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: 0.34 (0.28), residues: 831 helix: 0.82 (0.22), residues: 511 sheet: -3.27 (1.37), residues: 10 loop : -0.52 (0.33), residues: 310 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 0.011 0.001 PHE A 67 TYR 0.058 0.002 TYR D 80 ARG 0.010 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.05040 ( 658) hydrogen bonds : angle 3.41595 ( 1637) covalent geometry : bond 0.00422 (13814) covalent geometry : angle 0.74027 (19943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5023.99 seconds wall clock time: 87 minutes 50.82 seconds (5270.82 seconds total)