Starting phenix.real_space_refine on Sun Nov 17 02:38:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/11_2024/8cbq_16549.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/11_2024/8cbq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/11_2024/8cbq_16549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/11_2024/8cbq_16549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/11_2024/8cbq_16549.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/11_2024/8cbq_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-5513/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: 7.72, per 1000 atoms: 0.60 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: 3.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 6.66 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: 4.97 Time building geometry restraints manager: 3.65 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: 0.610 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: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.760 Find NCS groups from input model: 0.280 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.210 ------------------------------------------------------------------------------- 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= 0.477 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 *********************** 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 : 1.052 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: 0.3888 time to fit residues: 232.4933 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 : 1.022 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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= 0.238 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 *********************** 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 : 1.090 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: 0.8913 (m110) cc_final: 0.8688 (m110) REVERT: C 32 ARG cc_start: 0.7349 (ttp80) cc_final: 0.6548 (ttp80) REVERT: C 75 LYS cc_start: 0.8395 (mmmm) cc_final: 0.7935 (mmmm) REVERT: C 110 ASN cc_start: 0.8533 (t0) cc_final: 0.8015 (t0) REVERT: C 115 LEU cc_start: 0.9059 (mt) cc_final: 0.8764 (mp) REVERT: D 49 THR cc_start: 0.8534 (m) cc_final: 0.8182 (p) REVERT: D 59 MET cc_start: 0.9470 (mmm) cc_final: 0.8800 (tpp) REVERT: D 64 ASN cc_start: 0.8594 (m110) cc_final: 0.7928 (m110) REVERT: D 105 LYS cc_start: 0.8236 (tptp) cc_final: 0.8025 (tptp) REVERT: D 110 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7340 (mt-10) REVERT: F 25 ASN cc_start: 0.8641 (m-40) cc_final: 0.8247 (m-40) REVERT: F 39 ARG cc_start: 0.9045 (mmt-90) cc_final: 0.8641 (mmt180) REVERT: F 53 GLU cc_start: 0.8208 (tp30) cc_final: 0.7393 (tp30) REVERT: F 75 HIS cc_start: 0.8336 (t70) cc_final: 0.7845 (t70) REVERT: F 88 TYR cc_start: 0.9086 (m-10) cc_final: 0.8572 (m-80) REVERT: F 95 ARG cc_start: 0.8372 (mpp80) cc_final: 0.8022 (mtt90) REVERT: G 17 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7429 (ptp-170) REVERT: G 73 ASN cc_start: 0.8548 (t0) cc_final: 0.8329 (t0) REVERT: G 81 ARG cc_start: 0.8379 (tpt90) cc_final: 0.8173 (tpt90) REVERT: G 110 ASN cc_start: 0.8697 (t0) cc_final: 0.8212 (t0) REVERT: G 112 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8107 (mm110) REVERT: H 34 TYR cc_start: 0.7947 (m-80) cc_final: 0.7306 (m-10) REVERT: H 39 TYR cc_start: 0.8015 (t80) cc_final: 0.7773 (t80) REVERT: H 40 LYS cc_start: 0.8967 (tppt) cc_final: 0.8589 (tppt) REVERT: H 43 LYS cc_start: 0.8338 (pptt) cc_final: 0.7729 (pptt) REVERT: H 44 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8313 (mm-40) REVERT: H 102 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8037 (mm-30) REVERT: K 40 LEU cc_start: 0.3889 (OUTLIER) cc_final: 0.3487 (tp) REVERT: A 46 VAL cc_start: 0.9163 (t) cc_final: 0.8893 (t) REVERT: A 55 GLN cc_start: 0.8903 (mt0) cc_final: 0.8499 (tt0) REVERT: A 56 LYS cc_start: 0.7952 (pttp) cc_final: 0.7562 (pttt) REVERT: A 76 GLN cc_start: 0.8313 (mm110) cc_final: 0.7940 (mm-40) REVERT: A 79 LYS cc_start: 0.8920 (tptp) cc_final: 0.8698 (tptt) REVERT: A 106 ASP cc_start: 0.8503 (m-30) cc_final: 0.8173 (m-30) REVERT: A 129 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8229 (mmp80) REVERT: E 41 TYR cc_start: 0.7677 (m-80) cc_final: 0.7240 (m-80) REVERT: E 68 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7597 (pp30) REVERT: E 71 VAL cc_start: 0.9328 (t) cc_final: 0.9054 (t) REVERT: E 105 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7162 (tm-30) REVERT: E 113 HIS cc_start: 0.7807 (t70) cc_final: 0.7443 (t70) REVERT: E 117 VAL cc_start: 0.9137 (t) cc_final: 0.8929 (p) REVERT: E 119 ILE cc_start: 0.8873 (pt) cc_final: 0.7880 (pt) REVERT: E 120 MET cc_start: 0.6721 (mtt) cc_final: 0.6491 (mpp) REVERT: E 125 GLN cc_start: 0.8621 (mt0) cc_final: 0.8380 (mm-40) outliers start: 35 outliers final: 22 residues processed: 417 average time/residue: 0.3619 time to fit residues: 196.0141 Evaluate side-chains 387 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 364 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13814 Z= 0.282 Angle : 0.700 13.072 19943 Z= 0.396 Chirality : 0.037 0.198 2253 Planarity : 0.007 0.070 1485 Dihedral : 29.638 151.995 4242 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 7.15 % Allowed : 27.07 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.87 (0.27), residues: 831 helix: -0.10 (0.22), residues: 536 sheet: -4.14 (1.19), residues: 10 loop : -1.16 (0.32), residues: 285 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 F 61 TYR 0.018 0.002 TYR F 51 ARG 0.013 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 392 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: B 25 ASN cc_start: 0.8933 (m110) cc_final: 0.8602 (m-40) REVERT: B 35 ARG cc_start: 0.8773 (mtp85) cc_final: 0.8486 (mtp85) REVERT: B 39 ARG cc_start: 0.9104 (mmt-90) cc_final: 0.8637 (tpp80) REVERT: B 63 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7835 (mt-10) REVERT: C 75 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8467 (mmmm) REVERT: C 89 ASN cc_start: 0.8646 (m110) cc_final: 0.8412 (m-40) REVERT: C 95 LYS cc_start: 0.8949 (pttt) cc_final: 0.8489 (ptpp) REVERT: C 110 ASN cc_start: 0.8822 (t0) cc_final: 0.8412 (t0) REVERT: C 115 LEU cc_start: 0.8765 (mt) cc_final: 0.8445 (mm) REVERT: D 49 THR cc_start: 0.8504 (m) cc_final: 0.8242 (p) REVERT: D 59 MET cc_start: 0.9484 (mmm) cc_final: 0.9241 (tpp) REVERT: D 105 LYS cc_start: 0.8383 (tptp) cc_final: 0.8015 (tptp) REVERT: D 109 SER cc_start: 0.9256 (t) cc_final: 0.8829 (p) REVERT: D 110 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7494 (mt-10) REVERT: F 44 LYS cc_start: 0.8893 (mtmm) cc_final: 0.8407 (mtmm) REVERT: F 45 ARG cc_start: 0.9100 (mtp180) cc_final: 0.8430 (mmm-85) REVERT: F 53 GLU cc_start: 0.8234 (tp30) cc_final: 0.7776 (tp30) REVERT: F 88 TYR cc_start: 0.9248 (m-10) cc_final: 0.8735 (m-80) REVERT: F 95 ARG cc_start: 0.8481 (mpp80) cc_final: 0.8071 (mtt90) REVERT: G 17 ARG cc_start: 0.8430 (mtm180) cc_final: 0.8047 (ptp-170) REVERT: G 39 TYR cc_start: 0.8802 (m-80) cc_final: 0.8278 (m-80) REVERT: G 58 LEU cc_start: 0.8716 (mt) cc_final: 0.8353 (mp) REVERT: G 61 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7870 (mm-30) REVERT: G 68 ASN cc_start: 0.8204 (p0) cc_final: 0.7671 (p0) REVERT: G 78 ILE cc_start: 0.8836 (mt) cc_final: 0.8435 (mt) REVERT: G 95 LYS cc_start: 0.8912 (pttp) cc_final: 0.8593 (pttm) REVERT: H 34 TYR cc_start: 0.8146 (m-80) cc_final: 0.7723 (m-10) REVERT: H 40 LYS cc_start: 0.9383 (tppt) cc_final: 0.9021 (tppt) REVERT: H 99 LEU cc_start: 0.9115 (mp) cc_final: 0.8871 (mt) REVERT: H 102 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7524 (mm-30) REVERT: H 103 LEU cc_start: 0.9304 (mt) cc_final: 0.9073 (mt) REVERT: H 105 LYS cc_start: 0.8977 (ptmm) cc_final: 0.8634 (pttm) REVERT: K 40 LEU cc_start: 0.4262 (OUTLIER) cc_final: 0.4012 (tp) REVERT: A 79 LYS cc_start: 0.9159 (tptp) cc_final: 0.8841 (tptt) REVERT: A 90 MET cc_start: 0.9129 (mmm) cc_final: 0.8913 (mmm) REVERT: A 106 ASP cc_start: 0.8245 (m-30) cc_final: 0.7953 (m-30) REVERT: E 39 HIS cc_start: 0.4998 (p-80) cc_final: 0.4749 (p-80) REVERT: E 49 ARG cc_start: 0.8200 (ptp-170) cc_final: 0.7908 (ptm160) REVERT: E 67 PHE cc_start: 0.9034 (t80) cc_final: 0.8218 (t80) REVERT: E 68 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7888 (pp30) REVERT: E 73 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: E 105 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7137 (tm-30) REVERT: E 113 HIS cc_start: 0.7931 (t70) cc_final: 0.7727 (t70) REVERT: E 115 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8571 (mmmm) REVERT: E 120 MET cc_start: 0.7401 (mtt) cc_final: 0.6911 (mpp) outliers start: 51 outliers final: 32 residues processed: 410 average time/residue: 0.3666 time to fit residues: 194.9443 Evaluate side-chains 402 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 368 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 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 43 VAL 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 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 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.0470 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 0.0010 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 84 GLN G 73 ASN G 112 GLN H 92 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13814 Z= 0.205 Angle : 0.658 10.483 19943 Z= 0.372 Chirality : 0.036 0.210 2253 Planarity : 0.005 0.060 1485 Dihedral : 29.600 152.480 4239 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.35 % Allowed : 32.54 % Favored : 63.11 % 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: -0.04 (0.28), residues: 831 helix: 0.58 (0.22), residues: 532 sheet: -3.79 (1.46), residues: 10 loop : -0.90 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 82 HIS 0.003 0.001 HIS E 113 PHE 0.028 0.002 PHE A 67 TYR 0.019 0.002 TYR D 37 ARG 0.007 0.001 ARG F 92 *********************** 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 425 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 394 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: B 55 ARG cc_start: 0.8353 (mtt90) cc_final: 0.8048 (ttm110) REVERT: B 63 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7703 (mt-10) REVERT: C 89 ASN cc_start: 0.8614 (m110) cc_final: 0.8255 (m-40) REVERT: C 95 LYS cc_start: 0.8764 (pttt) cc_final: 0.8557 (pttp) REVERT: C 115 LEU cc_start: 0.8700 (mt) cc_final: 0.8347 (mm) REVERT: D 31 LYS cc_start: 0.8797 (mppt) cc_final: 0.8583 (mppt) REVERT: D 49 THR cc_start: 0.8562 (m) cc_final: 0.8072 (p) REVERT: D 59 MET cc_start: 0.9505 (mmm) cc_final: 0.9221 (tpp) REVERT: D 64 ASN cc_start: 0.8551 (m110) cc_final: 0.8224 (m-40) REVERT: D 105 LYS cc_start: 0.8491 (tptp) cc_final: 0.8057 (tptp) REVERT: D 109 SER cc_start: 0.9261 (t) cc_final: 0.8708 (p) REVERT: D 110 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7454 (mt-10) REVERT: F 44 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8311 (mtmm) REVERT: F 45 ARG cc_start: 0.8935 (mtp180) cc_final: 0.8362 (mmm-85) REVERT: F 67 ARG cc_start: 0.9074 (ttp80) cc_final: 0.8804 (ttp80) REVERT: F 70 VAL cc_start: 0.9122 (t) cc_final: 0.8773 (p) REVERT: F 88 TYR cc_start: 0.9149 (m-10) cc_final: 0.8631 (m-80) REVERT: F 95 ARG cc_start: 0.8410 (mpp80) cc_final: 0.8010 (mtt90) REVERT: G 20 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7677 (mtm180) REVERT: G 39 TYR cc_start: 0.8785 (m-80) cc_final: 0.8482 (m-80) REVERT: G 61 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7926 (mm-30) REVERT: G 78 ILE cc_start: 0.8843 (mt) cc_final: 0.8452 (mt) REVERT: G 81 ARG cc_start: 0.8689 (tpt90) cc_final: 0.8180 (tpt90) REVERT: G 85 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.8772 (mt) REVERT: H 34 TYR cc_start: 0.8093 (m-80) cc_final: 0.7669 (m-10) REVERT: H 40 LYS cc_start: 0.9311 (tppt) cc_final: 0.8957 (tptt) REVERT: H 43 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8406 (ptpt) REVERT: H 102 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7438 (mm-30) REVERT: H 105 LYS cc_start: 0.8954 (ptmm) cc_final: 0.8493 (pttm) REVERT: A 79 LYS cc_start: 0.9136 (tptp) cc_final: 0.8840 (tptp) REVERT: A 120 MET cc_start: 0.7514 (mmm) cc_final: 0.7264 (mmm) REVERT: E 60 LEU cc_start: 0.8975 (mm) cc_final: 0.7966 (mm) REVERT: E 68 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7803 (pp30) REVERT: E 73 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7577 (mm-30) REVERT: E 76 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8651 (tm-30) REVERT: E 85 GLN cc_start: 0.8177 (mt0) cc_final: 0.7779 (mt0) REVERT: E 93 GLN cc_start: 0.7479 (tm-30) cc_final: 0.6371 (tm-30) REVERT: E 94 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8014 (mt-10) REVERT: E 105 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7218 (tm-30) REVERT: E 113 HIS cc_start: 0.8207 (t70) cc_final: 0.7734 (t-90) REVERT: E 115 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8542 (mmmm) REVERT: E 120 MET cc_start: 0.7404 (mtt) cc_final: 0.7104 (mpp) outliers start: 31 outliers final: 21 residues processed: 402 average time/residue: 0.3594 time to fit residues: 188.3851 Evaluate side-chains 404 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 380 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain E residue 57 SER 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 1 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 0.0970 chunk 21 optimal weight: 0.0980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 89 ASN G 112 GLN H 64 ASN A 125 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13814 Z= 0.237 Angle : 0.667 8.259 19943 Z= 0.378 Chirality : 0.037 0.205 2253 Planarity : 0.005 0.060 1485 Dihedral : 29.554 150.877 4237 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.17 % Allowed : 32.12 % Favored : 61.71 % 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: 0.25 (0.28), residues: 831 helix: 0.80 (0.22), residues: 532 sheet: -3.66 (1.46), residues: 10 loop : -0.76 (0.34), residues: 289 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 0.015 0.001 PHE F 61 TYR 0.021 0.002 TYR E 99 ARG 0.008 0.001 ARG C 35 *********************** 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 433 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 389 time to evaluate : 1.089 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: B 31 LYS cc_start: 0.9193 (tptp) cc_final: 0.8935 (tptp) REVERT: B 39 ARG cc_start: 0.9193 (mmt-90) cc_final: 0.8972 (mmt90) REVERT: B 51 TYR cc_start: 0.7339 (m-80) cc_final: 0.7122 (m-80) REVERT: B 55 ARG cc_start: 0.8473 (mtt90) cc_final: 0.8198 (ttm110) REVERT: B 63 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7653 (mt-10) REVERT: B 79 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8714 (mmmm) REVERT: B 88 TYR cc_start: 0.8815 (m-10) cc_final: 0.7610 (m-10) REVERT: C 24 GLN cc_start: 0.8531 (mm-40) cc_final: 0.7847 (mm-40) REVERT: C 89 ASN cc_start: 0.8591 (m110) cc_final: 0.8251 (m110) REVERT: D 31 LYS cc_start: 0.8756 (mppt) cc_final: 0.8493 (mppt) REVERT: D 49 THR cc_start: 0.8886 (m) cc_final: 0.8594 (p) REVERT: D 59 MET cc_start: 0.9460 (mmm) cc_final: 0.9219 (tpp) REVERT: D 64 ASN cc_start: 0.8536 (m110) cc_final: 0.8231 (m-40) REVERT: D 105 LYS cc_start: 0.8437 (tptp) cc_final: 0.8102 (tptp) REVERT: D 109 SER cc_start: 0.9209 (t) cc_final: 0.8011 (p) REVERT: D 113 LYS cc_start: 0.8472 (mmtm) cc_final: 0.8151 (mmtm) REVERT: F 63 GLU cc_start: 0.7536 (pp20) cc_final: 0.6598 (pp20) REVERT: F 70 VAL cc_start: 0.9121 (t) cc_final: 0.8796 (p) REVERT: F 88 TYR cc_start: 0.9265 (m-10) cc_final: 0.8688 (m-80) REVERT: F 95 ARG cc_start: 0.8582 (mpp80) cc_final: 0.8282 (mtt90) REVERT: G 39 TYR cc_start: 0.8848 (m-80) cc_final: 0.8639 (m-80) REVERT: G 42 ARG cc_start: 0.8548 (mtm180) cc_final: 0.7955 (mtm180) REVERT: G 78 ILE cc_start: 0.9051 (mt) cc_final: 0.8662 (mt) REVERT: G 81 ARG cc_start: 0.8728 (tpt90) cc_final: 0.8271 (tpt90) REVERT: G 95 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8368 (pttm) REVERT: G 112 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8278 (mm110) REVERT: H 40 LYS cc_start: 0.9230 (tppt) cc_final: 0.8771 (tmtt) REVERT: H 43 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8368 (ptpt) REVERT: H 92 GLN cc_start: 0.8729 (tt0) cc_final: 0.8524 (tt0) REVERT: A 79 LYS cc_start: 0.9209 (tptp) cc_final: 0.8950 (tptp) REVERT: E 63 ARG cc_start: 0.7536 (mmp80) cc_final: 0.7267 (mmp80) REVERT: E 67 PHE cc_start: 0.8954 (t80) cc_final: 0.8208 (t80) REVERT: E 68 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7839 (pp30) REVERT: E 73 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7790 (tp30) REVERT: E 76 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8559 (tm-30) REVERT: E 79 LYS cc_start: 0.8252 (tppt) cc_final: 0.7724 (tptt) REVERT: E 85 GLN cc_start: 0.8104 (mt0) cc_final: 0.7893 (mt0) REVERT: E 105 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7290 (tm-30) REVERT: E 115 LYS cc_start: 0.8907 (ttmm) cc_final: 0.8534 (mmmm) outliers start: 44 outliers final: 38 residues processed: 402 average time/residue: 0.3656 time to fit residues: 190.9757 Evaluate side-chains 416 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 375 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 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 57 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 108 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.0270 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 89 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.6515 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= 0.221 Angle : 0.664 7.706 19943 Z= 0.374 Chirality : 0.036 0.214 2253 Planarity : 0.005 0.059 1485 Dihedral : 29.590 150.478 4237 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.87 % Allowed : 34.50 % Favored : 58.63 % 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: 1.01 (0.23), residues: 530 sheet: -3.50 (1.49), residues: 10 loop : -0.73 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 82 HIS 0.003 0.001 HIS E 113 PHE 0.027 0.001 PHE A 67 TYR 0.036 0.002 TYR D 80 ARG 0.012 0.001 ARG C 35 *********************** 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 432 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 383 time to evaluate : 1.109 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: 0.9189 (tptp) cc_final: 0.8962 (tptp) REVERT: B 39 ARG cc_start: 0.9331 (mmt-90) cc_final: 0.8837 (tpp-160) REVERT: B 44 LYS cc_start: 0.9077 (mttt) cc_final: 0.8664 (mttt) REVERT: B 55 ARG cc_start: 0.8515 (mtt90) cc_final: 0.8178 (ttm110) REVERT: B 63 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7731 (mt-10) REVERT: B 79 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8644 (mmmm) REVERT: C 24 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8087 (mm110) REVERT: C 29 ARG cc_start: 0.7811 (tpp80) cc_final: 0.6702 (tpp80) REVERT: C 32 ARG cc_start: 0.7120 (ttp-170) cc_final: 0.6682 (ttp-170) REVERT: C 75 LYS cc_start: 0.8810 (mmmm) cc_final: 0.8299 (mmmm) REVERT: C 84 GLN cc_start: 0.9239 (tp-100) cc_final: 0.9031 (tp-100) REVERT: C 89 ASN cc_start: 0.8549 (m110) cc_final: 0.8247 (m110) REVERT: D 31 LYS cc_start: 0.8791 (mppt) cc_final: 0.8366 (mmtm) REVERT: D 39 TYR cc_start: 0.7736 (t80) cc_final: 0.7220 (t80) REVERT: D 43 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8743 (tppt) REVERT: D 64 ASN cc_start: 0.8526 (m110) cc_final: 0.8189 (m-40) REVERT: D 76 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7676 (ttp80) REVERT: D 92 GLN cc_start: 0.7756 (pp30) cc_final: 0.7393 (pp30) REVERT: D 105 LYS cc_start: 0.8524 (tptp) cc_final: 0.8267 (tptp) REVERT: D 109 SER cc_start: 0.9209 (t) cc_final: 0.8938 (p) REVERT: F 53 GLU cc_start: 0.8145 (tp30) cc_final: 0.7812 (tp30) REVERT: F 63 GLU cc_start: 0.7678 (pp20) cc_final: 0.6815 (pp20) REVERT: F 70 VAL cc_start: 0.9108 (t) cc_final: 0.8754 (p) REVERT: F 75 HIS cc_start: 0.8445 (t70) cc_final: 0.7768 (t70) REVERT: F 78 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7720 (tpp80) REVERT: F 88 TYR cc_start: 0.9246 (m-10) cc_final: 0.8670 (m-80) REVERT: F 95 ARG cc_start: 0.8415 (mpp80) cc_final: 0.8136 (mtt90) REVERT: G 17 ARG cc_start: 0.8252 (mtt90) cc_final: 0.7973 (mtt90) REVERT: G 79 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8583 (mm) REVERT: G 81 ARG cc_start: 0.8821 (tpt90) cc_final: 0.8315 (tpt90) REVERT: G 85 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8727 (mt) REVERT: G 95 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8399 (pttm) REVERT: G 112 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8226 (mm110) REVERT: H 43 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8043 (ptpp) REVERT: H 73 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.6855 (mm-30) REVERT: H 113 LYS cc_start: 0.8692 (ptpt) cc_final: 0.8305 (ptpt) REVERT: A 49 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7925 (mtp-110) REVERT: A 76 GLN cc_start: 0.7407 (mt0) cc_final: 0.6985 (mt0) REVERT: A 79 LYS cc_start: 0.9270 (tptp) cc_final: 0.8984 (tptp) REVERT: A 105 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7898 (tm-30) REVERT: E 60 LEU cc_start: 0.9007 (mm) cc_final: 0.8054 (mm) REVERT: E 67 PHE cc_start: 0.8928 (t80) cc_final: 0.8286 (t80) REVERT: E 72 ARG cc_start: 0.8891 (tpp-160) cc_final: 0.8673 (mtm-85) REVERT: E 73 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: E 76 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8680 (tm-30) REVERT: E 85 GLN cc_start: 0.8325 (mt0) cc_final: 0.7991 (mt0) REVERT: E 93 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7177 (tm-30) REVERT: E 94 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7866 (mt-10) REVERT: E 105 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7232 (tm-30) REVERT: E 115 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8491 (mmmm) REVERT: E 128 ARG cc_start: 0.8858 (mtp180) cc_final: 0.8553 (mtp-110) outliers start: 49 outliers final: 31 residues processed: 398 average time/residue: 0.3609 time to fit residues: 186.4495 Evaluate side-chains 408 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 371 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 33 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain 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 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 38 ASN 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 85 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 89 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.7042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13814 Z= 0.334 Angle : 0.729 8.792 19943 Z= 0.407 Chirality : 0.039 0.206 2253 Planarity : 0.006 0.063 1485 Dihedral : 29.717 149.734 4237 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 8.13 % Allowed : 35.20 % Favored : 56.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.27), residues: 831 helix: 0.49 (0.22), residues: 532 sheet: -3.37 (1.50), residues: 10 loop : -0.80 (0.33), residues: 289 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 0.017 0.002 PHE F 61 TYR 0.041 0.003 TYR D 80 ARG 0.009 0.001 ARG F 92 *********************** 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 423 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 365 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 ARG cc_start: 0.9168 (mmt-90) cc_final: 0.8850 (mmt90) REVERT: B 44 LYS cc_start: 0.9324 (mttt) cc_final: 0.8923 (mttt) REVERT: B 63 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 79 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8563 (mmmm) REVERT: C 17 ARG cc_start: 0.8686 (mtp180) cc_final: 0.8135 (mtm110) REVERT: C 20 ARG cc_start: 0.7941 (mmt-90) cc_final: 0.7326 (mmt-90) REVERT: C 24 GLN cc_start: 0.8665 (mm-40) cc_final: 0.7998 (mm-40) REVERT: C 29 ARG cc_start: 0.7729 (tpp80) cc_final: 0.6711 (tpp80) REVERT: C 32 ARG cc_start: 0.7458 (ttp-170) cc_final: 0.6834 (ttp-170) REVERT: C 75 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8462 (mmmm) REVERT: C 84 GLN cc_start: 0.9165 (tp-100) cc_final: 0.8929 (tp-100) REVERT: C 89 ASN cc_start: 0.8544 (m110) cc_final: 0.8247 (m110) REVERT: D 31 LYS cc_start: 0.8780 (mppt) cc_final: 0.8365 (mmtm) REVERT: D 64 ASN cc_start: 0.8639 (m110) cc_final: 0.8312 (m110) REVERT: D 105 LYS cc_start: 0.8377 (tptp) cc_final: 0.8099 (tptp) REVERT: D 109 SER cc_start: 0.9143 (t) cc_final: 0.8914 (p) REVERT: F 63 GLU cc_start: 0.7901 (pp20) cc_final: 0.7156 (pp20) REVERT: F 70 VAL cc_start: 0.9191 (t) cc_final: 0.8937 (p) REVERT: F 74 GLU cc_start: 0.7506 (tp30) cc_final: 0.7256 (tp30) REVERT: F 88 TYR cc_start: 0.9390 (m-10) cc_final: 0.8726 (m-80) REVERT: G 18 SER cc_start: 0.8242 (m) cc_final: 0.7936 (p) REVERT: G 81 ARG cc_start: 0.8733 (tpt90) cc_final: 0.8444 (tpt90) REVERT: G 84 GLN cc_start: 0.9383 (tp-100) cc_final: 0.9124 (tp-100) REVERT: G 89 ASN cc_start: 0.8359 (m-40) cc_final: 0.7832 (m110) REVERT: G 112 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8309 (mm110) REVERT: H 29 THR cc_start: 0.8843 (t) cc_final: 0.8535 (m) REVERT: H 40 LYS cc_start: 0.8926 (tmtt) cc_final: 0.8508 (tptt) REVERT: H 89 ARG cc_start: 0.7532 (ptm-80) cc_final: 0.7218 (ptm-80) REVERT: H 92 GLN cc_start: 0.8824 (tt0) cc_final: 0.8622 (tt0) REVERT: H 113 LYS cc_start: 0.8727 (ptpt) cc_final: 0.8381 (ptpt) REVERT: A 49 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7989 (mtp-110) REVERT: A 76 GLN cc_start: 0.7445 (mt0) cc_final: 0.6955 (mt0) REVERT: A 79 LYS cc_start: 0.9270 (tptp) cc_final: 0.8949 (tptp) REVERT: A 106 ASP cc_start: 0.8173 (m-30) cc_final: 0.7948 (m-30) REVERT: E 56 LYS cc_start: 0.8288 (mmtm) cc_final: 0.7958 (mmtm) REVERT: E 68 GLN cc_start: 0.8191 (pp30) cc_final: 0.7825 (pp30) REVERT: E 73 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8194 (tp30) REVERT: E 76 GLN cc_start: 0.9193 (tm-30) cc_final: 0.8825 (tm-30) REVERT: E 85 GLN cc_start: 0.8474 (mt0) cc_final: 0.8212 (mt0) REVERT: E 105 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7398 (tm-30) REVERT: E 115 LYS cc_start: 0.8924 (ttmm) cc_final: 0.8518 (mmmm) outliers start: 58 outliers final: 43 residues processed: 383 average time/residue: 0.3483 time to fit residues: 174.1813 Evaluate side-chains 396 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 352 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE 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 52 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 GLU 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 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL 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 Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 73 ASN E 55 GLN E 108 ASN E 113 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.7303 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= 0.245 Angle : 0.723 12.891 19943 Z= 0.400 Chirality : 0.038 0.214 2253 Planarity : 0.005 0.062 1485 Dihedral : 29.708 149.834 4233 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.91 % Allowed : 40.67 % Favored : 54.42 % 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: 0.18 (0.28), residues: 831 helix: 0.75 (0.22), residues: 516 sheet: -3.46 (1.40), residues: 10 loop : -0.71 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.003 0.001 HIS E 113 PHE 0.026 0.001 PHE E 67 TYR 0.055 0.003 TYR D 80 ARG 0.014 0.001 ARG H 76 *********************** 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 417 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 382 time to evaluate : 1.113 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 44 LYS cc_start: 0.9329 (mttt) cc_final: 0.8554 (mttt) REVERT: B 63 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7649 (mt-10) REVERT: B 79 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8771 (mmmm) REVERT: B 98 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.7776 (m-10) REVERT: C 29 ARG cc_start: 0.7552 (tpp80) cc_final: 0.7093 (tpp80) REVERT: C 32 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.7112 (ttp-170) REVERT: C 75 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8458 (mmmm) REVERT: C 89 ASN cc_start: 0.8542 (m110) cc_final: 0.8206 (m110) REVERT: D 31 LYS cc_start: 0.8783 (mppt) cc_final: 0.8381 (mmtm) REVERT: D 39 TYR cc_start: 0.7880 (t80) cc_final: 0.7401 (t80) REVERT: D 43 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8317 (tppt) REVERT: D 64 ASN cc_start: 0.8551 (m110) cc_final: 0.8240 (m110) REVERT: D 105 LYS cc_start: 0.8411 (tptp) cc_final: 0.8147 (tptp) REVERT: D 109 SER cc_start: 0.9064 (t) cc_final: 0.8821 (p) REVERT: F 70 VAL cc_start: 0.9248 (t) cc_final: 0.8994 (p) REVERT: F 74 GLU cc_start: 0.7535 (tp30) cc_final: 0.7294 (tp30) REVERT: F 80 THR cc_start: 0.8690 (p) cc_final: 0.8412 (p) REVERT: F 88 TYR cc_start: 0.9269 (m-10) cc_final: 0.8659 (m-80) REVERT: F 95 ARG cc_start: 0.8592 (mpp80) cc_final: 0.8313 (mtt90) REVERT: G 18 SER cc_start: 0.8242 (m) cc_final: 0.7858 (p) REVERT: G 29 ARG cc_start: 0.7674 (tpp80) cc_final: 0.7205 (tpp80) REVERT: G 42 ARG cc_start: 0.8643 (mtm180) cc_final: 0.7511 (ptt-90) REVERT: G 81 ARG cc_start: 0.8804 (tpt90) cc_final: 0.8498 (tpt90) REVERT: G 84 GLN cc_start: 0.9380 (tp-100) cc_final: 0.9101 (tp-100) REVERT: G 85 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8203 (mt) REVERT: G 89 ASN cc_start: 0.8311 (m-40) cc_final: 0.7827 (m110) REVERT: G 112 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8172 (mm110) REVERT: H 29 THR cc_start: 0.8889 (t) cc_final: 0.8575 (m) REVERT: H 32 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7387 (tp30) REVERT: H 43 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7988 (ptpp) REVERT: H 76 ARG cc_start: 0.8792 (mtm110) cc_final: 0.8576 (mtm110) REVERT: H 92 GLN cc_start: 0.8770 (tt0) cc_final: 0.8520 (tt0) REVERT: A 41 TYR cc_start: 0.9034 (m-80) cc_final: 0.8816 (m-80) REVERT: A 42 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7370 (mmm160) REVERT: A 49 ARG cc_start: 0.8421 (mtp-110) cc_final: 0.8094 (mtp85) REVERT: A 76 GLN cc_start: 0.7404 (mt0) cc_final: 0.6881 (mt0) REVERT: A 79 LYS cc_start: 0.9253 (tptp) cc_final: 0.8678 (tptp) REVERT: A 97 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7461 (mm-30) REVERT: A 106 ASP cc_start: 0.7997 (m-30) cc_final: 0.7751 (m-30) REVERT: E 52 ARG cc_start: 0.8946 (ttm-80) cc_final: 0.8253 (ttm-80) REVERT: E 56 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7854 (mptt) REVERT: E 68 GLN cc_start: 0.8136 (pp30) cc_final: 0.7732 (pp30) REVERT: E 73 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8178 (tp30) REVERT: E 76 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8756 (tm-30) REVERT: E 85 GLN cc_start: 0.8127 (mt0) cc_final: 0.7716 (pt0) REVERT: E 93 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7265 (tm-30) REVERT: E 105 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7296 (tm-30) REVERT: E 115 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8507 (mmmm) outliers start: 35 outliers final: 27 residues processed: 390 average time/residue: 0.3685 time to fit residues: 185.7430 Evaluate side-chains 402 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 371 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain C residue 16 THR 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 97 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.7588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13814 Z= 0.250 Angle : 0.742 16.947 19943 Z= 0.405 Chirality : 0.038 0.215 2253 Planarity : 0.005 0.060 1485 Dihedral : 29.674 149.397 4233 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.05 % Allowed : 40.95 % Favored : 54.00 % 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: 0.21 (0.28), residues: 831 helix: 0.74 (0.22), residues: 517 sheet: -3.49 (1.36), residues: 10 loop : -0.65 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.003 0.001 HIS G 82 PHE 0.021 0.001 PHE E 67 TYR 0.072 0.003 TYR B 88 ARG 0.013 0.001 ARG H 76 *********************** 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 410 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 374 time to evaluate : 0.913 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 39 ARG cc_start: 0.9115 (mmp80) cc_final: 0.8075 (mmt90) REVERT: B 44 LYS cc_start: 0.8951 (mttt) cc_final: 0.8505 (mttt) REVERT: B 63 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 79 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8517 (mmmm) REVERT: C 17 ARG cc_start: 0.8833 (mtp180) cc_final: 0.8217 (mtm110) REVERT: C 25 PHE cc_start: 0.8510 (m-10) cc_final: 0.8309 (m-10) REVERT: C 29 ARG cc_start: 0.7483 (tpp80) cc_final: 0.6160 (tpp80) REVERT: C 32 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.6230 (ttp-170) REVERT: C 57 TYR cc_start: 0.8594 (t80) cc_final: 0.8240 (t80) REVERT: C 75 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8672 (mmmm) REVERT: C 108 LEU cc_start: 0.8676 (mt) cc_final: 0.8381 (tt) REVERT: D 31 LYS cc_start: 0.8831 (mppt) cc_final: 0.8462 (mmtm) REVERT: D 39 TYR cc_start: 0.7694 (t80) cc_final: 0.7227 (t80) REVERT: D 43 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8439 (tppt) REVERT: D 48 ASP cc_start: 0.8051 (m-30) cc_final: 0.7568 (p0) REVERT: D 64 ASN cc_start: 0.8567 (m110) cc_final: 0.8210 (m110) REVERT: D 105 LYS cc_start: 0.8397 (tptp) cc_final: 0.8079 (tptp) REVERT: D 109 SER cc_start: 0.9057 (t) cc_final: 0.8799 (p) REVERT: F 70 VAL cc_start: 0.9219 (t) cc_final: 0.8939 (p) REVERT: F 74 GLU cc_start: 0.7319 (tp30) cc_final: 0.7062 (tp30) REVERT: F 80 THR cc_start: 0.8729 (p) cc_final: 0.8484 (p) REVERT: F 88 TYR cc_start: 0.9278 (m-10) cc_final: 0.8697 (m-80) REVERT: G 18 SER cc_start: 0.8216 (m) cc_final: 0.7813 (p) REVERT: G 29 ARG cc_start: 0.7839 (tpp80) cc_final: 0.7370 (tpp80) REVERT: G 38 ASN cc_start: 0.8665 (m-40) cc_final: 0.7661 (t0) REVERT: G 81 ARG cc_start: 0.8807 (tpt90) cc_final: 0.8398 (tpt90) REVERT: G 89 ASN cc_start: 0.8288 (m-40) cc_final: 0.7939 (m110) REVERT: G 112 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8240 (mm110) REVERT: H 92 GLN cc_start: 0.8764 (tt0) cc_final: 0.8538 (tt0) REVERT: A 41 TYR cc_start: 0.9072 (m-80) cc_final: 0.8858 (m-80) REVERT: A 42 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7572 (mmm160) REVERT: A 76 GLN cc_start: 0.7390 (mt0) cc_final: 0.6901 (mt0) REVERT: A 97 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7654 (mm-30) REVERT: E 68 GLN cc_start: 0.8112 (pp30) cc_final: 0.7704 (pp30) REVERT: E 76 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8790 (tm-30) REVERT: E 85 GLN cc_start: 0.8019 (mt0) cc_final: 0.7662 (pt0) REVERT: E 105 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7378 (tm-30) REVERT: E 115 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8440 (mmmm) outliers start: 36 outliers final: 29 residues processed: 387 average time/residue: 0.3501 time to fit residues: 176.9548 Evaluate side-chains 394 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 365 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE 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 46 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 89 ASN D 106 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN E 108 ASN E 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.7788 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= 0.258 Angle : 0.778 16.479 19943 Z= 0.423 Chirality : 0.038 0.211 2253 Planarity : 0.006 0.084 1485 Dihedral : 29.719 148.857 4233 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.05 % Allowed : 42.08 % Favored : 52.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.28), residues: 831 helix: 0.67 (0.22), residues: 515 sheet: -3.37 (1.36), residues: 10 loop : -0.66 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.003 0.001 HIS G 82 PHE 0.031 0.001 PHE E 67 TYR 0.076 0.003 TYR B 88 ARG 0.017 0.001 ARG E 53 ********************** 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 402 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 366 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8864 (mtp85) cc_final: 0.8509 (ttm110) REVERT: B 39 ARG cc_start: 0.9175 (mmp80) cc_final: 0.8327 (mmt90) REVERT: B 44 LYS cc_start: 0.8758 (mttt) cc_final: 0.8316 (mttt) REVERT: B 63 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7669 (mt-10) REVERT: B 73 THR cc_start: 0.9247 (t) cc_final: 0.9036 (t) REVERT: B 79 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8501 (mmmm) REVERT: B 98 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.7619 (m-10) REVERT: C 17 ARG cc_start: 0.8823 (mtp180) cc_final: 0.8192 (mtm110) REVERT: C 29 ARG cc_start: 0.7657 (tpp80) cc_final: 0.7187 (tpp80) REVERT: C 32 ARG cc_start: 0.7335 (ttp-170) cc_final: 0.6838 (ttp80) REVERT: C 35 ARG cc_start: 0.7301 (tpp-160) cc_final: 0.6520 (mmt180) REVERT: C 36 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8598 (mtmt) REVERT: C 57 TYR cc_start: 0.8632 (t80) cc_final: 0.8266 (t80) REVERT: C 75 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8647 (mmmm) REVERT: D 31 LYS cc_start: 0.8894 (mppt) cc_final: 0.8527 (mmtm) REVERT: D 39 TYR cc_start: 0.7740 (t80) cc_final: 0.7308 (t80) REVERT: D 43 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8382 (tppt) REVERT: D 48 ASP cc_start: 0.8042 (m-30) cc_final: 0.7572 (p0) REVERT: D 64 ASN cc_start: 0.8598 (m110) cc_final: 0.8276 (m110) REVERT: D 73 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7630 (mm-30) REVERT: D 105 LYS cc_start: 0.8392 (tptp) cc_final: 0.8112 (tptp) REVERT: D 109 SER cc_start: 0.9053 (t) cc_final: 0.8798 (p) REVERT: D 117 LYS cc_start: 0.8825 (pptt) cc_final: 0.8419 (pptt) REVERT: F 70 VAL cc_start: 0.9229 (t) cc_final: 0.8984 (p) REVERT: F 88 TYR cc_start: 0.9268 (m-10) cc_final: 0.8700 (m-80) REVERT: G 18 SER cc_start: 0.8240 (m) cc_final: 0.7819 (p) REVERT: G 29 ARG cc_start: 0.7405 (tpp80) cc_final: 0.6640 (tpp80) REVERT: G 38 ASN cc_start: 0.8644 (m-40) cc_final: 0.7633 (t0) REVERT: G 81 ARG cc_start: 0.9006 (tpt90) cc_final: 0.8406 (tpt90) REVERT: G 89 ASN cc_start: 0.8085 (m-40) cc_final: 0.7773 (m110) REVERT: G 112 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8235 (mm110) REVERT: H 92 GLN cc_start: 0.8780 (tt0) cc_final: 0.8548 (tt0) REVERT: A 41 TYR cc_start: 0.9092 (m-80) cc_final: 0.8865 (m-80) REVERT: A 49 ARG cc_start: 0.8188 (mtp180) cc_final: 0.7285 (ttt180) REVERT: A 76 GLN cc_start: 0.7300 (mt0) cc_final: 0.6823 (mt0) REVERT: A 97 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7458 (mm-30) REVERT: E 50 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7480 (tm-30) REVERT: E 53 ARG cc_start: 0.8544 (tpt90) cc_final: 0.8338 (tmt-80) REVERT: E 56 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8149 (mmtm) REVERT: E 68 GLN cc_start: 0.8187 (pp30) cc_final: 0.7574 (pp30) REVERT: E 76 GLN cc_start: 0.9250 (tm-30) cc_final: 0.8859 (tm-30) REVERT: E 85 GLN cc_start: 0.7885 (mt0) cc_final: 0.7578 (pt0) REVERT: E 105 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7327 (tm-30) REVERT: E 115 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8443 (mmmm) outliers start: 36 outliers final: 30 residues processed: 378 average time/residue: 0.3472 time to fit residues: 172.0311 Evaluate side-chains 385 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 354 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain C residue 27 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 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 82 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE 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 46 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN E 108 ASN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.138586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095643 restraints weight = 31063.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.098644 restraints weight = 17535.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.100673 restraints weight = 12321.716| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.7984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13814 Z= 0.264 Angle : 0.771 15.882 19943 Z= 0.419 Chirality : 0.038 0.213 2253 Planarity : 0.006 0.062 1485 Dihedral : 29.721 148.422 4233 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.77 % Allowed : 43.06 % Favored : 52.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.27), residues: 831 helix: 0.60 (0.22), residues: 516 sheet: -3.35 (1.30), residues: 10 loop : -0.80 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.003 0.001 HIS G 82 PHE 0.020 0.001 PHE F 61 TYR 0.073 0.003 TYR B 88 ARG 0.012 0.001 ARG E 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3522.02 seconds wall clock time: 64 minutes 16.96 seconds (3856.96 seconds total)