Starting phenix.real_space_refine on Thu Jul 31 11:53:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbn_16546/07_2025/8cbn_16546.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbn_16546/07_2025/8cbn_16546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cbn_16546/07_2025/8cbn_16546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbn_16546/07_2025/8cbn_16546.map" model { file = "/net/cci-nas-00/data/ceres_data/8cbn_16546/07_2025/8cbn_16546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbn_16546/07_2025/8cbn_16546.cif" } resolution = 3.34 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 15 5.16 5 C 7698 2.51 5 N 2540 2.21 5 O 3116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13669 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3055 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3095 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "L" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 8.04, per 1000 atoms: 0.59 Number of scatterers: 13669 At special positions: 0 Unit cell: (81.144, 139.104, 129.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 300 15.00 O 3116 8.00 N 2540 7.00 C 7698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 1.4 seconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 58.1% alpha, 5.1% beta 125 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 7.16 Creating SS restraints... Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.520A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.790A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.647A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.516A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.542A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.586A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.957A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.734A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 102 through 122 removed outlier: 3.543A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.765A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.943A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.516A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.515A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.542A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.586A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.956A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.734A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 102 through 122 removed outlier: 3.543A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 87 removed outlier: 5.137A pdb=" N ASP K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN K 86 " --> pdb=" O TRP K 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.690A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.555A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.570A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.621A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.684A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.629A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 87 removed outlier: 5.136A pdb=" N ASP L 85 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN L 86 " --> pdb=" O TRP L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.151A pdb=" N ARG B 45 " --> pdb=" O ILE A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.434A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.172A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.168A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.144A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 50 through 51 removed outlier: 3.622A pdb=" N PHE K 43 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA K 13 " --> pdb=" O TRP K 21 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA K 23 " --> pdb=" O ILE K 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE K 11 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 50 through 51 removed outlier: 3.623A pdb=" N PHE L 43 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA L 13 " --> pdb=" O TRP L 21 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA L 23 " --> pdb=" O ILE L 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE L 11 " --> pdb=" O ALA L 23 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 5.32 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2357 1.33 - 1.45: 4911 1.45 - 1.57: 6654 1.57 - 1.69: 598 1.69 - 1.81: 30 Bond restraints: 14550 Sorted by residual: bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.757 0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.763 0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.52e+00 bond pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" CB ARG F 78 " pdb=" CG ARG F 78 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 ... (remaining 14545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 19913 1.59 - 3.18: 951 3.18 - 4.78: 51 4.78 - 6.37: 13 6.37 - 7.96: 7 Bond angle restraints: 20935 Sorted by residual: angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 120.20 125.90 -5.70 1.50e+00 4.44e-01 1.45e+01 angle pdb=" C SER L 62 " pdb=" N GLU L 63 " pdb=" CA GLU L 63 " ideal model delta sigma weight residual 122.61 128.15 -5.54 1.56e+00 4.11e-01 1.26e+01 angle pdb=" C SER K 62 " pdb=" N GLU K 63 " pdb=" CA GLU K 63 " ideal model delta sigma weight residual 122.61 128.14 -5.53 1.56e+00 4.11e-01 1.26e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 120.20 125.02 -4.82 1.50e+00 4.44e-01 1.03e+01 angle pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " pdb=" P DC I 35 " ideal model delta sigma weight residual 120.20 124.97 -4.77 1.50e+00 4.44e-01 1.01e+01 ... (remaining 20930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 6580 34.29 - 68.57: 1388 68.57 - 102.86: 15 102.86 - 137.15: 2 137.15 - 171.44: 1 Dihedral angle restraints: 7986 sinusoidal: 5267 harmonic: 2719 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 48.56 171.44 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU K 53 " pdb=" C LEU K 53 " pdb=" N GLY K 54 " pdb=" CA GLY K 54 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1293 0.035 - 0.070: 832 0.070 - 0.105: 172 0.105 - 0.140: 40 0.140 - 0.175: 10 Chirality restraints: 2347 Sorted by residual: chirality pdb=" P DC I 21 " pdb=" OP1 DC I 21 " pdb=" OP2 DC I 21 " pdb=" O5' DC I 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.52 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB VAL L 90 " pdb=" CA VAL L 90 " pdb=" CG1 VAL L 90 " pdb=" CG2 VAL L 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 2344 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO E 66 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO G 80 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO C 80 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.037 5.00e-02 4.00e+02 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.68: 2 1.68 - 2.49: 54 2.49 - 3.29: 12951 3.29 - 4.10: 39079 4.10 - 4.90: 66074 Warning: very small nonbonded interaction distances. Nonbonded interactions: 118160 Sorted by model distance: nonbonded pdb=" OP1 DA I -69 " pdb=" NZ LYS L 73 " model vdw 0.876 3.120 nonbonded pdb=" OP1 DA I -69 " pdb=" CE LYS L 73 " model vdw 0.936 3.440 nonbonded pdb=" OP1 DG I -68 " pdb=" CD PRO L 19 " model vdw 1.751 3.440 nonbonded pdb=" O3' DA I -69 " pdb=" NH2 ARG L 74 " model vdw 1.840 3.120 nonbonded pdb=" P DA I -69 " pdb=" CE LYS L 73 " model vdw 1.967 3.800 ... (remaining 118155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 37.390 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 14550 Z= 0.361 Angle : 0.720 7.960 20935 Z= 0.424 Chirality : 0.044 0.175 2347 Planarity : 0.007 0.069 1614 Dihedral : 25.785 171.435 6230 Min Nonbonded Distance : 0.876 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.28 % Allowed : 8.75 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.72 (0.17), residues: 913 helix: -4.46 (0.09), residues: 538 sheet: -4.09 (0.69), residues: 34 loop : -2.16 (0.26), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP L 82 HIS 0.004 0.001 HIS L 20 PHE 0.013 0.002 PHE K 45 TYR 0.012 0.002 TYR B 72 ARG 0.004 0.001 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.31427 ( 667) hydrogen bonds : angle 10.67049 ( 1658) covalent geometry : bond 0.00816 (14550) covalent geometry : angle 0.72022 (20935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 310 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.8817 (mttt) cc_final: 0.8467 (mttp) REVERT: B 98 TYR cc_start: 0.8973 (m-10) cc_final: 0.8159 (m-10) REVERT: C 34 LEU cc_start: 0.8953 (mt) cc_final: 0.8726 (mm) REVERT: C 110 ASN cc_start: 0.8654 (t0) cc_final: 0.8437 (t0) REVERT: C 115 LEU cc_start: 0.8384 (mt) cc_final: 0.7998 (mp) REVERT: D 59 MET cc_start: 0.8367 (mmm) cc_final: 0.8047 (mmm) REVERT: D 91 ILE cc_start: 0.8561 (mm) cc_final: 0.8306 (mt) REVERT: D 103 LEU cc_start: 0.8637 (mt) cc_final: 0.8277 (mt) REVERT: F 43 VAL cc_start: 0.9461 (t) cc_final: 0.9260 (t) REVERT: F 73 THR cc_start: 0.7936 (m) cc_final: 0.7699 (m) REVERT: H 87 THR cc_start: 0.8808 (p) cc_final: 0.8441 (t) REVERT: A 90 MET cc_start: 0.8080 (mmm) cc_final: 0.7870 (mmt) REVERT: A 120 MET cc_start: 0.7883 (mtp) cc_final: 0.7414 (mtt) REVERT: A 126 LEU cc_start: 0.9415 (tp) cc_final: 0.9168 (tp) REVERT: E 41 TYR cc_start: 0.8515 (m-80) cc_final: 0.8265 (m-10) REVERT: E 60 LEU cc_start: 0.8938 (mt) cc_final: 0.8699 (mt) REVERT: E 119 ILE cc_start: 0.9261 (pt) cc_final: 0.9011 (pt) REVERT: E 125 GLN cc_start: 0.8627 (mt0) cc_final: 0.8360 (mt0) outliers start: 18 outliers final: 7 residues processed: 323 average time/residue: 0.4758 time to fit residues: 196.0916 Evaluate side-chains 240 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 233 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 73 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 68 ASN C 73 ASN D 44 GLN D 92 GLN F 18 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 92 GLN K 64 ASN K 86 ASN A 108 ASN A 113 HIS L 64 ASN L 86 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.166510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103599 restraints weight = 20742.417| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.53 r_work: 0.2992 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14550 Z= 0.180 Angle : 0.632 9.171 20935 Z= 0.373 Chirality : 0.038 0.175 2347 Planarity : 0.006 0.056 1614 Dihedral : 29.653 156.167 4342 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.77 % Allowed : 17.36 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.47 (0.24), residues: 913 helix: -1.57 (0.19), residues: 549 sheet: -4.29 (0.91), residues: 20 loop : -1.28 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.008 0.001 HIS E 39 PHE 0.014 0.001 PHE A 67 TYR 0.013 0.002 TYR C 57 ARG 0.008 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.06682 ( 667) hydrogen bonds : angle 3.27353 ( 1658) covalent geometry : bond 0.00395 (14550) covalent geometry : angle 0.63195 (20935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 261 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9296 (mttt) cc_final: 0.8856 (mttp) REVERT: B 93 GLN cc_start: 0.8957 (mt0) cc_final: 0.8674 (mt0) REVERT: B 98 TYR cc_start: 0.9028 (m-10) cc_final: 0.8417 (m-10) REVERT: C 34 LEU cc_start: 0.8963 (mt) cc_final: 0.8412 (mt) REVERT: C 73 ASN cc_start: 0.7539 (t0) cc_final: 0.6777 (t0) REVERT: C 115 LEU cc_start: 0.8600 (mt) cc_final: 0.8265 (mp) REVERT: D 59 MET cc_start: 0.8924 (mmm) cc_final: 0.8435 (mmt) REVERT: D 68 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: F 58 LEU cc_start: 0.8516 (tp) cc_final: 0.8289 (tp) REVERT: F 73 THR cc_start: 0.8867 (m) cc_final: 0.8512 (m) REVERT: F 74 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: F 84 MET cc_start: 0.8648 (mmm) cc_final: 0.8408 (mmm) REVERT: G 71 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8226 (ttp80) REVERT: G 92 GLU cc_start: 0.8473 (pm20) cc_final: 0.8138 (pm20) REVERT: G 110 ASN cc_start: 0.8818 (t0) cc_final: 0.8531 (t0) REVERT: H 51 ILE cc_start: 0.9084 (tt) cc_final: 0.8883 (tt) REVERT: H 68 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8466 (mm-30) REVERT: H 87 THR cc_start: 0.8458 (p) cc_final: 0.7943 (m) REVERT: H 109 SER cc_start: 0.9050 (t) cc_final: 0.8845 (p) REVERT: H 117 LYS cc_start: 0.8485 (tppp) cc_final: 0.7840 (ttpp) REVERT: K 14 LYS cc_start: 0.6473 (tppt) cc_final: 0.6230 (tppt) REVERT: K 70 LYS cc_start: 0.4034 (mmtm) cc_final: 0.3833 (mmtm) REVERT: A 79 LYS cc_start: 0.9035 (tttm) cc_final: 0.8495 (tttp) REVERT: A 90 MET cc_start: 0.8568 (mmm) cc_final: 0.8156 (mmp) REVERT: A 118 THR cc_start: 0.9531 (m) cc_final: 0.9265 (p) REVERT: A 120 MET cc_start: 0.7848 (mtp) cc_final: 0.7617 (mtp) REVERT: E 39 HIS cc_start: 0.8598 (t70) cc_final: 0.8188 (t70) REVERT: E 41 TYR cc_start: 0.8486 (m-80) cc_final: 0.8246 (m-10) REVERT: E 76 GLN cc_start: 0.9270 (tp40) cc_final: 0.9015 (mm-40) REVERT: E 94 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8722 (mm-30) REVERT: E 105 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8904 (mm-30) REVERT: E 119 ILE cc_start: 0.9408 (pt) cc_final: 0.9177 (pt) outliers start: 14 outliers final: 8 residues processed: 271 average time/residue: 0.3750 time to fit residues: 138.2548 Evaluate side-chains 252 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 241 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 50 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS A 39 HIS E 93 GLN L 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.161743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098267 restraints weight = 20556.766| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.45 r_work: 0.2926 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14550 Z= 0.173 Angle : 0.578 8.336 20935 Z= 0.339 Chirality : 0.035 0.127 2347 Planarity : 0.005 0.048 1614 Dihedral : 29.399 150.232 4329 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.17 % Allowed : 20.28 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.26), residues: 913 helix: 0.13 (0.22), residues: 553 sheet: -3.67 (0.99), residues: 24 loop : -1.35 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 82 HIS 0.004 0.001 HIS E 39 PHE 0.012 0.001 PHE E 67 TYR 0.028 0.002 TYR H 80 ARG 0.008 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.05839 ( 667) hydrogen bonds : angle 2.84919 ( 1658) covalent geometry : bond 0.00383 (14550) covalent geometry : angle 0.57831 (20935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 266 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9483 (mttt) cc_final: 0.9016 (mttp) REVERT: B 84 MET cc_start: 0.8058 (mmt) cc_final: 0.7611 (mmt) REVERT: B 93 GLN cc_start: 0.8962 (mt0) cc_final: 0.8739 (mt0) REVERT: B 98 TYR cc_start: 0.9174 (m-10) cc_final: 0.8585 (m-10) REVERT: C 73 ASN cc_start: 0.7494 (t0) cc_final: 0.7033 (t0) REVERT: C 94 ASN cc_start: 0.8420 (t0) cc_final: 0.7952 (t0) REVERT: D 73 GLU cc_start: 0.9230 (tp30) cc_final: 0.8973 (tp30) REVERT: D 76 ARG cc_start: 0.8653 (ttm110) cc_final: 0.8377 (ttm-80) REVERT: D 117 LYS cc_start: 0.8986 (tppp) cc_final: 0.8558 (tptm) REVERT: D 122 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.6284 (ttpp) REVERT: F 63 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8517 (mt-10) REVERT: F 73 THR cc_start: 0.9072 (m) cc_final: 0.8725 (m) REVERT: F 78 ARG cc_start: 0.9072 (mtt90) cc_final: 0.8745 (mtm-85) REVERT: G 33 LEU cc_start: 0.8775 (mt) cc_final: 0.8552 (mt) REVERT: G 35 ARG cc_start: 0.8831 (ttm110) cc_final: 0.8596 (ttm110) REVERT: G 39 TYR cc_start: 0.9255 (m-80) cc_final: 0.8631 (m-80) REVERT: G 73 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8075 (t0) REVERT: H 87 THR cc_start: 0.8992 (p) cc_final: 0.8784 (t) REVERT: H 90 GLU cc_start: 0.8914 (mp0) cc_final: 0.8640 (mp0) REVERT: H 117 LYS cc_start: 0.8543 (tppp) cc_final: 0.7937 (ttpp) REVERT: K 16 LYS cc_start: 0.8259 (tppt) cc_final: 0.7957 (tppt) REVERT: K 70 LYS cc_start: 0.4118 (mmtm) cc_final: 0.3860 (mmtm) REVERT: A 59 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7786 (mp0) REVERT: A 79 LYS cc_start: 0.9146 (tttm) cc_final: 0.8906 (tttm) REVERT: A 90 MET cc_start: 0.8528 (mmm) cc_final: 0.8248 (mmt) REVERT: A 120 MET cc_start: 0.7996 (mtp) cc_final: 0.7752 (mtp) REVERT: E 39 HIS cc_start: 0.8866 (t70) cc_final: 0.8302 (t70) REVERT: E 41 TYR cc_start: 0.8988 (m-80) cc_final: 0.8539 (m-10) REVERT: E 45 THR cc_start: 0.8746 (t) cc_final: 0.8496 (p) REVERT: E 59 GLU cc_start: 0.8644 (mp0) cc_final: 0.7962 (mp0) REVERT: E 76 GLN cc_start: 0.9276 (tp40) cc_final: 0.8924 (mm-40) REVERT: E 119 ILE cc_start: 0.9333 (pt) cc_final: 0.9118 (pt) outliers start: 25 outliers final: 15 residues processed: 277 average time/residue: 0.3342 time to fit residues: 123.8851 Evaluate side-chains 261 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 14 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 84 optimal weight: 40.0000 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 112 GLN D 46 HIS F 25 ASN F 75 HIS F 93 GLN K 78 ASN A 39 HIS E 93 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.090666 restraints weight = 20899.858| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.73 r_work: 0.2805 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14550 Z= 0.190 Angle : 0.589 8.114 20935 Z= 0.343 Chirality : 0.036 0.128 2347 Planarity : 0.004 0.047 1614 Dihedral : 29.375 150.264 4327 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.18 % Allowed : 22.56 % Favored : 73.26 % 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: 913 helix: 0.83 (0.23), residues: 548 sheet: -4.02 (0.92), residues: 20 loop : -1.03 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 82 HIS 0.004 0.001 HIS K 20 PHE 0.011 0.001 PHE E 67 TYR 0.043 0.002 TYR D 80 ARG 0.009 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.05764 ( 667) hydrogen bonds : angle 2.89638 ( 1658) covalent geometry : bond 0.00431 (14550) covalent geometry : angle 0.58912 (20935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8759 (mm-30) REVERT: B 77 LYS cc_start: 0.9489 (mttt) cc_final: 0.9126 (mttp) REVERT: B 84 MET cc_start: 0.8014 (mmt) cc_final: 0.7719 (mmt) REVERT: B 98 TYR cc_start: 0.9156 (m-10) cc_final: 0.8611 (m-10) REVERT: C 73 ASN cc_start: 0.7786 (t0) cc_final: 0.7161 (t0) REVERT: C 94 ASN cc_start: 0.8140 (t0) cc_final: 0.7636 (t0) REVERT: C 100 VAL cc_start: 0.9784 (OUTLIER) cc_final: 0.9403 (p) REVERT: D 76 ARG cc_start: 0.8386 (ttm110) cc_final: 0.8113 (ttm-80) REVERT: D 102 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7114 (mm-30) REVERT: D 105 LYS cc_start: 0.9024 (tppp) cc_final: 0.8654 (mtmm) REVERT: D 122 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6836 (ttpp) REVERT: F 73 THR cc_start: 0.9023 (m) cc_final: 0.8671 (m) REVERT: F 78 ARG cc_start: 0.9108 (mtt90) cc_final: 0.8790 (mtm-85) REVERT: G 39 TYR cc_start: 0.9223 (m-80) cc_final: 0.8886 (m-80) REVERT: G 75 LYS cc_start: 0.8411 (mmtp) cc_final: 0.8123 (mmtm) REVERT: G 90 ASP cc_start: 0.8838 (t70) cc_final: 0.7700 (t0) REVERT: G 92 GLU cc_start: 0.8368 (pm20) cc_final: 0.8047 (pm20) REVERT: H 68 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8563 (mm-30) REVERT: H 80 TYR cc_start: 0.8675 (m-80) cc_final: 0.8187 (m-80) REVERT: H 87 THR cc_start: 0.8925 (p) cc_final: 0.8645 (t) REVERT: H 90 GLU cc_start: 0.8952 (mp0) cc_final: 0.8516 (mp0) REVERT: H 117 LYS cc_start: 0.8444 (tppp) cc_final: 0.7829 (ttpp) REVERT: K 14 LYS cc_start: 0.6172 (tppt) cc_final: 0.3829 (mptt) REVERT: K 16 LYS cc_start: 0.8354 (tppt) cc_final: 0.7956 (mmmt) REVERT: K 70 LYS cc_start: 0.4074 (mmtm) cc_final: 0.3815 (mmtm) REVERT: A 57 SER cc_start: 0.8993 (p) cc_final: 0.8757 (t) REVERT: A 79 LYS cc_start: 0.8999 (tttm) cc_final: 0.8661 (tttp) REVERT: A 85 GLN cc_start: 0.8573 (mt0) cc_final: 0.8210 (mt0) REVERT: A 90 MET cc_start: 0.8330 (mmm) cc_final: 0.7933 (mmp) REVERT: A 120 MET cc_start: 0.8006 (mtp) cc_final: 0.7762 (mtp) REVERT: E 39 HIS cc_start: 0.9150 (t70) cc_final: 0.8380 (t70) REVERT: E 45 THR cc_start: 0.8886 (t) cc_final: 0.8473 (p) REVERT: E 54 TYR cc_start: 0.8724 (m-80) cc_final: 0.8460 (m-80) REVERT: E 76 GLN cc_start: 0.9214 (tp40) cc_final: 0.8945 (mm-40) REVERT: E 105 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8862 (mm-30) outliers start: 33 outliers final: 23 residues processed: 277 average time/residue: 0.3242 time to fit residues: 121.1363 Evaluate side-chains 281 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 32 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN G 73 ASN E 93 GLN E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.088715 restraints weight = 21104.990| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.77 r_work: 0.2781 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14550 Z= 0.194 Angle : 0.584 7.625 20935 Z= 0.340 Chirality : 0.036 0.129 2347 Planarity : 0.004 0.047 1614 Dihedral : 29.258 147.492 4327 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.45 % Allowed : 24.33 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.28), residues: 913 helix: 1.26 (0.23), residues: 547 sheet: -3.49 (0.95), residues: 24 loop : -0.98 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 82 HIS 0.006 0.001 HIS A 39 PHE 0.011 0.001 PHE E 67 TYR 0.028 0.002 TYR D 80 ARG 0.006 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.05776 ( 667) hydrogen bonds : angle 2.88317 ( 1658) covalent geometry : bond 0.00438 (14550) covalent geometry : angle 0.58437 (20935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 272 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9522 (mttt) cc_final: 0.9223 (mttm) REVERT: B 98 TYR cc_start: 0.9187 (m-10) cc_final: 0.8639 (m-10) REVERT: C 38 ASN cc_start: 0.8587 (m-40) cc_final: 0.8297 (m-40) REVERT: C 73 ASN cc_start: 0.8284 (t0) cc_final: 0.7476 (t0) REVERT: C 77 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7711 (tpp80) REVERT: C 91 GLU cc_start: 0.8439 (mp0) cc_final: 0.8081 (tp30) REVERT: D 91 ILE cc_start: 0.8851 (mm) cc_final: 0.8517 (mt) REVERT: D 102 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: D 105 LYS cc_start: 0.9020 (tppp) cc_final: 0.8614 (mtmm) REVERT: F 78 ARG cc_start: 0.9150 (mtt90) cc_final: 0.8861 (mtm-85) REVERT: G 39 TYR cc_start: 0.9220 (m-80) cc_final: 0.8701 (m-80) REVERT: G 73 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8070 (t0) REVERT: G 75 LYS cc_start: 0.8587 (mmtp) cc_final: 0.8269 (mmtm) REVERT: G 90 ASP cc_start: 0.8419 (t70) cc_final: 0.7597 (t0) REVERT: G 92 GLU cc_start: 0.8419 (pm20) cc_final: 0.8066 (pm20) REVERT: H 80 TYR cc_start: 0.8735 (m-80) cc_final: 0.8257 (m-80) REVERT: H 84 SER cc_start: 0.8896 (m) cc_final: 0.8351 (p) REVERT: H 117 LYS cc_start: 0.8419 (tppp) cc_final: 0.7838 (ttpp) REVERT: K 16 LYS cc_start: 0.8474 (tppt) cc_final: 0.8044 (tptp) REVERT: K 70 LYS cc_start: 0.4026 (mmtm) cc_final: 0.3804 (mmtm) REVERT: A 42 ARG cc_start: 0.7509 (mmm-85) cc_final: 0.7084 (mmm160) REVERT: A 57 SER cc_start: 0.9174 (p) cc_final: 0.8959 (t) REVERT: A 79 LYS cc_start: 0.9133 (tttm) cc_final: 0.8925 (tttm) REVERT: A 90 MET cc_start: 0.8335 (mmm) cc_final: 0.8022 (mmt) REVERT: A 108 ASN cc_start: 0.8958 (t0) cc_final: 0.8313 (t0) REVERT: A 120 MET cc_start: 0.8112 (mtp) cc_final: 0.7482 (mtp) REVERT: A 123 ASP cc_start: 0.9186 (m-30) cc_final: 0.8829 (m-30) REVERT: E 39 HIS cc_start: 0.9292 (t70) cc_final: 0.8668 (t70) REVERT: E 45 THR cc_start: 0.9113 (t) cc_final: 0.8860 (m) REVERT: E 54 TYR cc_start: 0.8609 (m-80) cc_final: 0.8179 (m-80) REVERT: E 73 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8268 (tt0) REVERT: E 105 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8907 (mm-30) REVERT: E 124 ILE cc_start: 0.8676 (mt) cc_final: 0.8440 (mm) outliers start: 43 outliers final: 32 residues processed: 289 average time/residue: 0.3115 time to fit residues: 121.7048 Evaluate side-chains 300 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.156115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.090600 restraints weight = 21761.990| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.76 r_work: 0.2856 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14550 Z= 0.178 Angle : 0.571 7.283 20935 Z= 0.333 Chirality : 0.035 0.151 2347 Planarity : 0.004 0.049 1614 Dihedral : 29.141 146.752 4323 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.82 % Allowed : 25.86 % Favored : 69.33 % 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: 0.73 (0.28), residues: 913 helix: 1.52 (0.23), residues: 551 sheet: -3.92 (0.96), residues: 20 loop : -0.94 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.003 0.001 HIS G 31 PHE 0.010 0.001 PHE E 67 TYR 0.052 0.002 TYR D 80 ARG 0.004 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.05487 ( 667) hydrogen bonds : angle 2.78820 ( 1658) covalent geometry : bond 0.00400 (14550) covalent geometry : angle 0.57124 (20935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9583 (mttt) cc_final: 0.9281 (mttm) REVERT: B 98 TYR cc_start: 0.9197 (m-10) cc_final: 0.8667 (m-10) REVERT: C 73 ASN cc_start: 0.8607 (t0) cc_final: 0.8007 (t0) REVERT: C 75 LYS cc_start: 0.9130 (mmtp) cc_final: 0.8845 (mmmm) REVERT: C 77 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8066 (tpp80) REVERT: C 100 VAL cc_start: 0.9508 (t) cc_final: 0.9010 (p) REVERT: D 43 LYS cc_start: 0.8789 (tppt) cc_final: 0.8588 (tppt) REVERT: D 91 ILE cc_start: 0.8958 (mm) cc_final: 0.8652 (mt) REVERT: D 102 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: D 105 LYS cc_start: 0.9118 (tppp) cc_final: 0.8721 (mtmm) REVERT: F 84 MET cc_start: 0.7915 (mmm) cc_final: 0.7505 (mmm) REVERT: G 39 TYR cc_start: 0.9192 (m-80) cc_final: 0.8691 (m-80) REVERT: G 73 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8327 (t0) REVERT: G 75 LYS cc_start: 0.8717 (mmtp) cc_final: 0.8498 (mmtm) REVERT: G 90 ASP cc_start: 0.8481 (t70) cc_final: 0.7302 (t70) REVERT: G 92 GLU cc_start: 0.8639 (pm20) cc_final: 0.8155 (pm20) REVERT: G 93 LEU cc_start: 0.8182 (mt) cc_final: 0.7936 (mm) REVERT: H 84 SER cc_start: 0.9041 (m) cc_final: 0.8523 (p) REVERT: H 105 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9091 (mmmm) REVERT: H 117 LYS cc_start: 0.8712 (tppp) cc_final: 0.8162 (ttpp) REVERT: K 16 LYS cc_start: 0.8583 (tppt) cc_final: 0.8144 (tptp) REVERT: K 70 LYS cc_start: 0.4177 (mmtm) cc_final: 0.3951 (mmtm) REVERT: A 42 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7201 (mmm160) REVERT: A 57 SER cc_start: 0.9300 (p) cc_final: 0.8806 (t) REVERT: A 59 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7888 (mp0) REVERT: A 79 LYS cc_start: 0.9146 (tttm) cc_final: 0.8803 (tttp) REVERT: A 85 GLN cc_start: 0.8647 (mt0) cc_final: 0.8328 (mt0) REVERT: A 90 MET cc_start: 0.8290 (mmm) cc_final: 0.8026 (mmt) REVERT: A 120 MET cc_start: 0.8360 (mtp) cc_final: 0.7743 (mtp) REVERT: A 123 ASP cc_start: 0.9165 (m-30) cc_final: 0.8831 (m-30) REVERT: E 39 HIS cc_start: 0.9073 (t70) cc_final: 0.8436 (t-90) REVERT: E 45 THR cc_start: 0.9252 (t) cc_final: 0.9044 (m) REVERT: E 54 TYR cc_start: 0.8882 (m-80) cc_final: 0.8416 (m-80) REVERT: E 105 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8885 (mm-30) REVERT: E 108 ASN cc_start: 0.9215 (t0) cc_final: 0.8899 (t0) REVERT: E 124 ILE cc_start: 0.8883 (mt) cc_final: 0.8632 (mm) outliers start: 38 outliers final: 28 residues processed: 280 average time/residue: 0.3115 time to fit residues: 118.4339 Evaluate side-chains 289 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 4 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.091751 restraints weight = 21776.376| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.75 r_work: 0.2855 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14550 Z= 0.159 Angle : 0.566 8.162 20935 Z= 0.328 Chirality : 0.034 0.146 2347 Planarity : 0.004 0.045 1614 Dihedral : 29.021 145.997 4323 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.68 % Allowed : 28.39 % Favored : 67.93 % 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: 0.95 (0.28), residues: 913 helix: 1.74 (0.23), residues: 551 sheet: -3.98 (0.97), residues: 20 loop : -0.92 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP L 21 HIS 0.003 0.001 HIS E 113 PHE 0.011 0.001 PHE E 67 TYR 0.043 0.002 TYR D 80 ARG 0.004 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.05204 ( 667) hydrogen bonds : angle 2.69764 ( 1658) covalent geometry : bond 0.00354 (14550) covalent geometry : angle 0.56553 (20935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 263 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9571 (mttt) cc_final: 0.9277 (mttm) REVERT: B 98 TYR cc_start: 0.9182 (m-10) cc_final: 0.8670 (m-10) REVERT: C 73 ASN cc_start: 0.8521 (t0) cc_final: 0.7957 (t0) REVERT: C 100 VAL cc_start: 0.9516 (t) cc_final: 0.9050 (p) REVERT: D 49 THR cc_start: 0.9040 (m) cc_final: 0.8839 (p) REVERT: D 102 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7711 (mm-30) REVERT: D 105 LYS cc_start: 0.9106 (tppp) cc_final: 0.8726 (mtmm) REVERT: F 84 MET cc_start: 0.8057 (mmm) cc_final: 0.7466 (mmm) REVERT: G 39 TYR cc_start: 0.9181 (m-80) cc_final: 0.8685 (m-80) REVERT: G 90 ASP cc_start: 0.8166 (t70) cc_final: 0.7056 (t70) REVERT: G 92 GLU cc_start: 0.8670 (pm20) cc_final: 0.8216 (pm20) REVERT: H 84 SER cc_start: 0.8995 (m) cc_final: 0.8466 (p) REVERT: H 105 LYS cc_start: 0.9322 (mmmm) cc_final: 0.9089 (mmmm) REVERT: H 117 LYS cc_start: 0.8716 (tppp) cc_final: 0.8214 (ttpp) REVERT: K 14 LYS cc_start: 0.6391 (tppt) cc_final: 0.4211 (mmtt) REVERT: K 16 LYS cc_start: 0.8628 (tppt) cc_final: 0.7967 (tptm) REVERT: K 70 LYS cc_start: 0.4610 (mmtm) cc_final: 0.4384 (mmtm) REVERT: A 42 ARG cc_start: 0.7610 (mmm-85) cc_final: 0.7183 (mmm160) REVERT: A 79 LYS cc_start: 0.9056 (tttm) cc_final: 0.8834 (tttp) REVERT: A 85 GLN cc_start: 0.8651 (mt0) cc_final: 0.8325 (mt0) REVERT: A 90 MET cc_start: 0.8136 (mmm) cc_final: 0.7876 (mmt) REVERT: A 108 ASN cc_start: 0.8881 (t0) cc_final: 0.8379 (t0) REVERT: A 120 MET cc_start: 0.8295 (mtp) cc_final: 0.8031 (mtp) REVERT: E 39 HIS cc_start: 0.9034 (t70) cc_final: 0.8506 (t-90) REVERT: E 45 THR cc_start: 0.9233 (t) cc_final: 0.8979 (m) REVERT: E 105 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8822 (mm-30) REVERT: E 124 ILE cc_start: 0.8864 (mt) cc_final: 0.8610 (mm) outliers start: 29 outliers final: 25 residues processed: 275 average time/residue: 0.3389 time to fit residues: 124.7627 Evaluate side-chains 282 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 102 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089740 restraints weight = 21834.237| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.74 r_work: 0.2844 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14550 Z= 0.187 Angle : 0.584 7.434 20935 Z= 0.338 Chirality : 0.036 0.137 2347 Planarity : 0.004 0.044 1614 Dihedral : 29.094 145.184 4323 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.69 % Allowed : 26.62 % Favored : 68.69 % 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: 0.99 (0.28), residues: 913 helix: 1.78 (0.23), residues: 553 sheet: -3.78 (0.97), residues: 20 loop : -0.97 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 21 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.047 0.002 TYR D 80 ARG 0.004 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.05712 ( 667) hydrogen bonds : angle 2.84923 ( 1658) covalent geometry : bond 0.00424 (14550) covalent geometry : angle 0.58402 (20935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9577 (mttt) cc_final: 0.9324 (mttm) REVERT: B 98 TYR cc_start: 0.9193 (m-10) cc_final: 0.8696 (m-10) REVERT: C 15 LYS cc_start: 0.7632 (mtmm) cc_final: 0.7300 (mtmm) REVERT: C 36 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8636 (mmmm) REVERT: C 73 ASN cc_start: 0.8582 (t0) cc_final: 0.7992 (t0) REVERT: C 100 VAL cc_start: 0.9511 (t) cc_final: 0.8997 (p) REVERT: D 91 ILE cc_start: 0.8954 (mm) cc_final: 0.8660 (mt) REVERT: D 102 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: D 105 LYS cc_start: 0.9142 (tppp) cc_final: 0.8689 (mtmm) REVERT: F 52 GLU cc_start: 0.9140 (tp30) cc_final: 0.8690 (tp30) REVERT: G 39 TYR cc_start: 0.9200 (m-80) cc_final: 0.8804 (m-80) REVERT: G 73 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8754 (t0) REVERT: G 90 ASP cc_start: 0.8721 (t70) cc_final: 0.8312 (t70) REVERT: G 92 GLU cc_start: 0.8649 (pm20) cc_final: 0.8342 (pm20) REVERT: H 84 SER cc_start: 0.9032 (m) cc_final: 0.8476 (p) REVERT: H 105 LYS cc_start: 0.9331 (mmmm) cc_final: 0.9131 (mmmm) REVERT: H 117 LYS cc_start: 0.8742 (tppp) cc_final: 0.8230 (ttpp) REVERT: K 14 LYS cc_start: 0.6431 (tppt) cc_final: 0.4223 (mmtt) REVERT: K 16 LYS cc_start: 0.8698 (tppt) cc_final: 0.8272 (tptm) REVERT: K 70 LYS cc_start: 0.4640 (mmtm) cc_final: 0.4379 (mmtm) REVERT: A 42 ARG cc_start: 0.7704 (mmm-85) cc_final: 0.7274 (mmm160) REVERT: A 59 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7910 (mp0) REVERT: A 85 GLN cc_start: 0.8695 (mt0) cc_final: 0.8344 (mt0) REVERT: A 90 MET cc_start: 0.8269 (mmm) cc_final: 0.7992 (mmt) REVERT: A 120 MET cc_start: 0.8440 (mtp) cc_final: 0.7873 (mtp) REVERT: A 123 ASP cc_start: 0.9163 (m-30) cc_final: 0.8825 (m-30) REVERT: E 39 HIS cc_start: 0.9015 (t70) cc_final: 0.8611 (t70) REVERT: E 105 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8816 (mm-30) REVERT: E 108 ASN cc_start: 0.9180 (t0) cc_final: 0.8850 (t0) REVERT: E 124 ILE cc_start: 0.8906 (mt) cc_final: 0.8665 (mm) outliers start: 37 outliers final: 28 residues processed: 279 average time/residue: 0.3200 time to fit residues: 121.1103 Evaluate side-chains 289 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 96 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.156248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.090775 restraints weight = 21732.155| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.76 r_work: 0.2859 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14550 Z= 0.169 Angle : 0.573 7.403 20935 Z= 0.333 Chirality : 0.035 0.179 2347 Planarity : 0.004 0.044 1614 Dihedral : 29.002 144.926 4323 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.06 % Allowed : 28.14 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.12 (0.28), residues: 913 helix: 1.91 (0.23), residues: 553 sheet: -3.74 (0.98), residues: 20 loop : -0.95 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 21 HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.042 0.002 TYR D 80 ARG 0.004 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.05375 ( 667) hydrogen bonds : angle 2.79496 ( 1658) covalent geometry : bond 0.00379 (14550) covalent geometry : angle 0.57339 (20935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9581 (mttt) cc_final: 0.9327 (mttm) REVERT: B 98 TYR cc_start: 0.9192 (m-10) cc_final: 0.8696 (m-10) REVERT: C 15 LYS cc_start: 0.7593 (mtmm) cc_final: 0.7257 (mtmm) REVERT: C 73 ASN cc_start: 0.8549 (t0) cc_final: 0.7997 (t0) REVERT: C 100 VAL cc_start: 0.9390 (t) cc_final: 0.8788 (p) REVERT: D 102 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: D 105 LYS cc_start: 0.9115 (tppp) cc_final: 0.8693 (mtmm) REVERT: F 84 MET cc_start: 0.8029 (mmm) cc_final: 0.7550 (mmm) REVERT: G 39 TYR cc_start: 0.9217 (m-80) cc_final: 0.8715 (m-80) REVERT: G 73 ASN cc_start: 0.9209 (OUTLIER) cc_final: 0.8959 (t0) REVERT: G 74 LYS cc_start: 0.9477 (tppp) cc_final: 0.9267 (tppp) REVERT: G 90 ASP cc_start: 0.8389 (t70) cc_final: 0.7541 (t70) REVERT: G 92 GLU cc_start: 0.8609 (pm20) cc_final: 0.8129 (pm20) REVERT: G 110 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8840 (t0) REVERT: H 84 SER cc_start: 0.9071 (m) cc_final: 0.8533 (p) REVERT: H 117 LYS cc_start: 0.8740 (tppp) cc_final: 0.8232 (ttpp) REVERT: K 14 LYS cc_start: 0.6422 (tppt) cc_final: 0.4245 (mmtt) REVERT: K 16 LYS cc_start: 0.8691 (tppt) cc_final: 0.8251 (tptp) REVERT: K 70 LYS cc_start: 0.4589 (mmtm) cc_final: 0.4333 (mmtm) REVERT: A 42 ARG cc_start: 0.7703 (mmm-85) cc_final: 0.7229 (mmm160) REVERT: A 59 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7916 (mp0) REVERT: A 85 GLN cc_start: 0.8700 (mt0) cc_final: 0.8336 (mt0) REVERT: A 90 MET cc_start: 0.8160 (mmm) cc_final: 0.7905 (mmt) REVERT: A 108 ASN cc_start: 0.9115 (t0) cc_final: 0.8558 (t0) REVERT: A 120 MET cc_start: 0.8427 (mtp) cc_final: 0.8175 (mtp) REVERT: E 39 HIS cc_start: 0.9024 (t70) cc_final: 0.8606 (t70) REVERT: E 105 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.8858 (mm-30) REVERT: E 108 ASN cc_start: 0.9191 (t0) cc_final: 0.8856 (t0) REVERT: E 124 ILE cc_start: 0.8897 (mt) cc_final: 0.8651 (mm) outliers start: 32 outliers final: 27 residues processed: 275 average time/residue: 0.3430 time to fit residues: 131.0326 Evaluate side-chains 289 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.156780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.091237 restraints weight = 21725.399| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.74 r_work: 0.2867 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14550 Z= 0.163 Angle : 0.574 8.213 20935 Z= 0.333 Chirality : 0.035 0.137 2347 Planarity : 0.004 0.044 1614 Dihedral : 28.999 144.656 4323 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.80 % Allowed : 28.26 % Favored : 67.93 % 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: 1.23 (0.28), residues: 913 helix: 2.03 (0.23), residues: 553 sheet: -3.75 (0.97), residues: 20 loop : -0.98 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 21 HIS 0.004 0.001 HIS E 113 PHE 0.013 0.001 PHE E 67 TYR 0.039 0.002 TYR D 80 ARG 0.005 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.05304 ( 667) hydrogen bonds : angle 2.76495 ( 1658) covalent geometry : bond 0.00365 (14550) covalent geometry : angle 0.57365 (20935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9571 (mttt) cc_final: 0.9320 (mttm) REVERT: B 92 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8669 (ttt-90) REVERT: B 98 TYR cc_start: 0.9185 (m-10) cc_final: 0.8686 (m-10) REVERT: C 15 LYS cc_start: 0.7546 (mtmm) cc_final: 0.7201 (mtmm) REVERT: C 73 ASN cc_start: 0.8520 (t0) cc_final: 0.7973 (t0) REVERT: C 100 VAL cc_start: 0.9385 (t) cc_final: 0.8775 (p) REVERT: D 102 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: D 105 LYS cc_start: 0.9116 (tppp) cc_final: 0.8695 (mtmm) REVERT: F 84 MET cc_start: 0.8122 (mmm) cc_final: 0.7515 (mmm) REVERT: G 39 TYR cc_start: 0.9206 (m-80) cc_final: 0.8783 (m-80) REVERT: G 90 ASP cc_start: 0.8440 (t70) cc_final: 0.7532 (t70) REVERT: G 92 GLU cc_start: 0.8616 (pm20) cc_final: 0.8028 (pm20) REVERT: G 110 ASN cc_start: 0.9079 (t0) cc_final: 0.8832 (t0) REVERT: H 84 SER cc_start: 0.9062 (m) cc_final: 0.8527 (p) REVERT: H 117 LYS cc_start: 0.8745 (tppp) cc_final: 0.8241 (ttpp) REVERT: K 14 LYS cc_start: 0.6603 (tppt) cc_final: 0.4533 (mmtt) REVERT: K 16 LYS cc_start: 0.8720 (tppt) cc_final: 0.8307 (tptp) REVERT: K 70 LYS cc_start: 0.4594 (mmtm) cc_final: 0.4240 (mmtm) REVERT: A 42 ARG cc_start: 0.7661 (mmm-85) cc_final: 0.7182 (mmm160) REVERT: A 59 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7938 (mp0) REVERT: A 85 GLN cc_start: 0.8693 (mt0) cc_final: 0.8318 (mt0) REVERT: A 90 MET cc_start: 0.8158 (mmm) cc_final: 0.7884 (mmt) REVERT: A 120 MET cc_start: 0.8405 (mtp) cc_final: 0.8158 (mtp) REVERT: E 39 HIS cc_start: 0.9034 (t70) cc_final: 0.8520 (t70) REVERT: E 73 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8524 (tt0) REVERT: E 105 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8877 (mm-30) REVERT: E 124 ILE cc_start: 0.8889 (mt) cc_final: 0.8640 (mm) outliers start: 30 outliers final: 27 residues processed: 269 average time/residue: 0.4001 time to fit residues: 146.4641 Evaluate side-chains 285 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 3 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.153498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.088110 restraints weight = 22096.750| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.71 r_work: 0.2811 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.6674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14550 Z= 0.226 Angle : 0.620 8.799 20935 Z= 0.356 Chirality : 0.038 0.186 2347 Planarity : 0.004 0.043 1614 Dihedral : 29.206 144.337 4323 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.56 % Allowed : 27.76 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.28), residues: 913 helix: 1.77 (0.22), residues: 553 sheet: -3.73 (0.95), residues: 20 loop : -1.04 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP K 21 HIS 0.005 0.001 HIS G 31 PHE 0.013 0.001 PHE E 67 TYR 0.048 0.002 TYR D 80 ARG 0.005 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.06246 ( 667) hydrogen bonds : angle 3.01846 ( 1658) covalent geometry : bond 0.00522 (14550) covalent geometry : angle 0.61966 (20935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8241.08 seconds wall clock time: 146 minutes 58.32 seconds (8818.32 seconds total)