Starting phenix.real_space_refine on Sun Nov 17 09:53:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/11_2024/8cbn_16546.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/11_2024/8cbn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/11_2024/8cbn_16546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/11_2024/8cbn_16546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/11_2024/8cbn_16546.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbn_16546/11_2024/8cbn_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-5513/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: 7.66, per 1000 atoms: 0.56 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: 3.02 Conformation dependent library (CDL) restraints added in 1.1 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: 6.85 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: 5.15 Time building geometry restraints manager: 3.62 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: 0.700 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.070 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- 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= 0.468 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 *********************** 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 : 0.991 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: 0.4353 time to fit residues: 179.3625 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 : 1.046 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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= 0.220 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 *********************** 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 : 0.952 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: 0.9157 (mttt) cc_final: 0.8788 (mttp) REVERT: B 93 GLN cc_start: 0.8553 (mt0) cc_final: 0.8291 (mt0) REVERT: B 98 TYR cc_start: 0.8925 (m-10) cc_final: 0.8269 (m-10) REVERT: C 34 LEU cc_start: 0.8970 (mt) cc_final: 0.8505 (mt) REVERT: C 73 ASN cc_start: 0.7916 (t0) cc_final: 0.7112 (t0) REVERT: C 115 LEU cc_start: 0.8632 (mt) cc_final: 0.8378 (mp) REVERT: D 59 MET cc_start: 0.8615 (mmm) cc_final: 0.8145 (mmt) REVERT: D 68 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: F 73 THR cc_start: 0.8849 (m) cc_final: 0.8513 (m) REVERT: F 74 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: G 71 ARG cc_start: 0.8226 (ttp80) cc_final: 0.7899 (ttp80) REVERT: G 110 ASN cc_start: 0.8444 (t0) cc_final: 0.8220 (t0) REVERT: H 51 ILE cc_start: 0.9118 (tt) cc_final: 0.8917 (tt) REVERT: H 87 THR cc_start: 0.8481 (p) cc_final: 0.7900 (m) REVERT: H 117 LYS cc_start: 0.8945 (tppp) cc_final: 0.8618 (ttpp) REVERT: K 14 LYS cc_start: 0.5846 (tppt) cc_final: 0.5590 (tppt) REVERT: A 79 LYS cc_start: 0.8991 (tttm) cc_final: 0.8402 (tttp) REVERT: A 90 MET cc_start: 0.8078 (mmm) cc_final: 0.7758 (mmp) REVERT: A 118 THR cc_start: 0.9410 (m) cc_final: 0.9165 (p) REVERT: A 120 MET cc_start: 0.7786 (mtp) cc_final: 0.7525 (mtp) REVERT: A 130 ILE cc_start: 0.9163 (mm) cc_final: 0.8959 (mm) REVERT: E 94 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8087 (mm-30) REVERT: E 119 ILE cc_start: 0.9338 (pt) cc_final: 0.9126 (pt) REVERT: E 126 LEU cc_start: 0.8746 (tp) cc_final: 0.8530 (tt) outliers start: 14 outliers final: 8 residues processed: 271 average time/residue: 0.3337 time to fit residues: 121.3969 Evaluate side-chains 250 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 240 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 60 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 50.0000 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 116 optimal weight: 20.0000 chunk 96 optimal weight: 0.3980 chunk 107 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4535 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= 0.243 Angle : 0.599 8.518 20935 Z= 0.349 Chirality : 0.036 0.142 2347 Planarity : 0.005 0.049 1614 Dihedral : 29.470 148.643 4329 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.17 % Allowed : 20.79 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.26), residues: 913 helix: 0.12 (0.22), residues: 552 sheet: -3.69 (0.98), residues: 24 loop : -1.36 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.007 0.001 HIS E 39 PHE 0.013 0.001 PHE E 67 TYR 0.031 0.002 TYR H 80 ARG 0.007 0.001 ARG A 42 *********************** 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 293 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 0.999 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: 0.9459 (mttt) cc_final: 0.9072 (mttp) REVERT: B 93 GLN cc_start: 0.8650 (mt0) cc_final: 0.8436 (mt0) REVERT: B 98 TYR cc_start: 0.9129 (m-10) cc_final: 0.8495 (m-10) REVERT: C 73 ASN cc_start: 0.8116 (t0) cc_final: 0.7404 (t0) REVERT: C 94 ASN cc_start: 0.8844 (t0) cc_final: 0.8302 (t0) REVERT: D 73 GLU cc_start: 0.8896 (tp30) cc_final: 0.8650 (tp30) REVERT: D 76 ARG cc_start: 0.8763 (ttm110) cc_final: 0.8560 (ttm-80) REVERT: D 102 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6440 (mm-30) REVERT: F 43 VAL cc_start: 0.9194 (t) cc_final: 0.8976 (m) REVERT: F 63 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8462 (mt-10) REVERT: F 88 TYR cc_start: 0.8975 (m-10) cc_final: 0.8546 (m-80) REVERT: G 33 LEU cc_start: 0.9019 (mt) cc_final: 0.8752 (mt) REVERT: H 64 ASN cc_start: 0.9128 (m-40) cc_final: 0.8894 (m-40) REVERT: H 117 LYS cc_start: 0.8998 (tppp) cc_final: 0.8715 (ttpp) REVERT: A 42 ARG cc_start: 0.7364 (mmm-85) cc_final: 0.6700 (mmm-85) REVERT: A 79 LYS cc_start: 0.9099 (tttm) cc_final: 0.8837 (tttm) REVERT: A 85 GLN cc_start: 0.8536 (mt0) cc_final: 0.8331 (mt0) REVERT: A 90 MET cc_start: 0.8281 (mmm) cc_final: 0.8056 (mmp) REVERT: A 120 MET cc_start: 0.7998 (mtp) cc_final: 0.7733 (mtp) REVERT: E 45 THR cc_start: 0.9040 (t) cc_final: 0.8657 (p) REVERT: E 54 TYR cc_start: 0.9226 (m-80) cc_final: 0.9021 (m-80) REVERT: E 59 GLU cc_start: 0.8256 (mp0) cc_final: 0.7662 (mp0) outliers start: 25 outliers final: 15 residues processed: 279 average time/residue: 0.3434 time to fit residues: 127.1814 Evaluate side-chains 258 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 243 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR 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 F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU 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 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain E residue 80 THR 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 106 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN F 25 ASN F 75 HIS F 93 GLN G 73 ASN K 78 ASN A 39 HIS E 39 HIS E 93 GLN E 108 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5006 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= 0.230 Angle : 0.585 8.107 20935 Z= 0.341 Chirality : 0.036 0.136 2347 Planarity : 0.004 0.047 1614 Dihedral : 29.386 150.505 4323 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.56 % Allowed : 23.83 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.27), residues: 913 helix: 0.84 (0.22), residues: 548 sheet: -4.15 (0.92), residues: 20 loop : -1.07 (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 D 106 PHE 0.012 0.001 PHE E 67 TYR 0.047 0.002 TYR D 80 ARG 0.007 0.001 ARG A 40 *********************** 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 298 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 1.201 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 74 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7893 (mm-30) REVERT: B 77 LYS cc_start: 0.9472 (mttt) cc_final: 0.9182 (mttp) REVERT: B 98 TYR cc_start: 0.9127 (m-10) cc_final: 0.8480 (m-10) REVERT: C 73 ASN cc_start: 0.8472 (t0) cc_final: 0.7639 (t0) REVERT: C 94 ASN cc_start: 0.8764 (t0) cc_final: 0.8194 (t0) REVERT: D 76 ARG cc_start: 0.8773 (ttm110) cc_final: 0.8480 (ttm-80) REVERT: D 102 GLU cc_start: 0.7703 (mm-30) cc_final: 0.6772 (mm-30) REVERT: F 25 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7673 (m-40) REVERT: F 35 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8144 (ttt-90) REVERT: G 33 LEU cc_start: 0.9057 (mt) cc_final: 0.8792 (mt) REVERT: G 39 TYR cc_start: 0.8899 (m-80) cc_final: 0.8673 (m-80) REVERT: G 75 LYS cc_start: 0.8957 (mmtp) cc_final: 0.8645 (mmtm) REVERT: H 64 ASN cc_start: 0.9095 (m-40) cc_final: 0.8842 (m-40) REVERT: H 117 LYS cc_start: 0.8972 (tppp) cc_final: 0.8761 (ttpp) REVERT: K 50 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.7033 (m) REVERT: A 79 LYS cc_start: 0.8984 (tttm) cc_final: 0.8574 (tttp) REVERT: A 90 MET cc_start: 0.7914 (mmm) cc_final: 0.7644 (mmp) REVERT: A 120 MET cc_start: 0.7997 (mtp) cc_final: 0.7783 (mtp) REVERT: E 45 THR cc_start: 0.9104 (t) cc_final: 0.8712 (p) REVERT: E 54 TYR cc_start: 0.9095 (m-80) cc_final: 0.8797 (m-80) REVERT: E 73 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8120 (tt0) REVERT: E 105 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8439 (mm-30) outliers start: 36 outliers final: 27 residues processed: 278 average time/residue: 0.3373 time to fit residues: 125.6773 Evaluate side-chains 279 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 249 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 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 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 25 ASN 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 H residue 53 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 112 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN A 39 HIS ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14550 Z= 0.320 Angle : 0.626 7.933 20935 Z= 0.361 Chirality : 0.038 0.159 2347 Planarity : 0.005 0.044 1614 Dihedral : 29.452 148.077 4323 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.32 % Allowed : 24.46 % 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: 0.23 (0.28), residues: 913 helix: 1.10 (0.23), residues: 548 sheet: -3.52 (0.96), residues: 24 loop : -1.08 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.014 0.001 HIS A 39 PHE 0.011 0.001 PHE E 67 TYR 0.055 0.002 TYR D 80 ARG 0.007 0.001 ARG G 71 *********************** 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 297 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 1.119 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 88 TYR cc_start: 0.8748 (m-10) cc_final: 0.8521 (m-10) REVERT: B 98 TYR cc_start: 0.9102 (m-10) cc_final: 0.8528 (m-10) REVERT: C 61 GLU cc_start: 0.8173 (tp30) cc_final: 0.7967 (tp30) REVERT: C 73 ASN cc_start: 0.8965 (t0) cc_final: 0.8208 (t0) REVERT: C 77 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.8014 (tpp80) REVERT: D 76 ARG cc_start: 0.8670 (ttm110) cc_final: 0.8356 (ttm-80) REVERT: D 105 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8219 (mtmm) REVERT: D 117 LYS cc_start: 0.9284 (tppp) cc_final: 0.8967 (ttmm) REVERT: G 73 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8553 (t0) REVERT: G 75 LYS cc_start: 0.9078 (mmtp) cc_final: 0.8772 (mmtm) REVERT: G 90 ASP cc_start: 0.8706 (t70) cc_final: 0.8090 (t0) REVERT: H 64 ASN cc_start: 0.9088 (m-40) cc_final: 0.8754 (m-40) REVERT: H 80 TYR cc_start: 0.9021 (m-80) cc_final: 0.8674 (m-80) REVERT: K 14 LYS cc_start: 0.5318 (tppt) cc_final: 0.3271 (mmtt) REVERT: K 50 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.7301 (m) REVERT: A 42 ARG cc_start: 0.7665 (mmm-85) cc_final: 0.7256 (mmm-85) REVERT: A 79 LYS cc_start: 0.9088 (tttm) cc_final: 0.8842 (tttm) REVERT: A 108 ASN cc_start: 0.9216 (t0) cc_final: 0.8555 (t0) REVERT: A 120 MET cc_start: 0.8237 (mtp) cc_final: 0.7695 (mtp) REVERT: A 123 ASP cc_start: 0.8839 (m-30) cc_final: 0.8531 (m-30) REVERT: E 45 THR cc_start: 0.9286 (t) cc_final: 0.8919 (m) REVERT: E 54 TYR cc_start: 0.9120 (m-80) cc_final: 0.8662 (m-80) REVERT: E 73 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8141 (tt0) outliers start: 42 outliers final: 35 residues processed: 273 average time/residue: 0.3369 time to fit residues: 123.5228 Evaluate side-chains 288 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 30 VAL 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 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 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 25 ASN 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 F residue 97 LEU Chi-restraints excluded: chain G residue 73 ASN 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 H residue 87 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain E residue 39 HIS 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 L residue 65 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 115 optimal weight: 40.0000 chunk 95 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 25 ASN G 73 ASN A 39 HIS E 39 HIS E 93 GLN E 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14550 Z= 0.216 Angle : 0.576 7.549 20935 Z= 0.336 Chirality : 0.035 0.138 2347 Planarity : 0.004 0.043 1614 Dihedral : 29.208 147.664 4323 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.45 % Allowed : 25.48 % Favored : 69.07 % 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: 0.65 (0.28), residues: 913 helix: 1.45 (0.23), residues: 547 sheet: -4.08 (0.96), residues: 20 loop : -0.91 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.010 0.001 HIS A 39 PHE 0.012 0.001 PHE E 67 TYR 0.043 0.002 TYR D 80 ARG 0.008 0.000 ARG G 71 *********************** 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 308 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7962 (mm-30) REVERT: B 98 TYR cc_start: 0.9054 (m-10) cc_final: 0.8516 (m-10) REVERT: C 73 ASN cc_start: 0.8889 (t0) cc_final: 0.8159 (t0) REVERT: C 75 LYS cc_start: 0.9273 (mmtp) cc_final: 0.8986 (mmmm) REVERT: D 91 ILE cc_start: 0.9012 (mm) cc_final: 0.8741 (mt) REVERT: D 102 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7607 (mm-30) REVERT: D 117 LYS cc_start: 0.9269 (tppp) cc_final: 0.8988 (ttmm) REVERT: F 39 ARG cc_start: 0.8821 (mmt90) cc_final: 0.8614 (tpp-160) REVERT: F 84 MET cc_start: 0.7583 (mmm) cc_final: 0.7015 (mmm) REVERT: G 73 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8534 (t0) REVERT: G 90 ASP cc_start: 0.8661 (t70) cc_final: 0.8116 (t0) REVERT: H 64 ASN cc_start: 0.8982 (m-40) cc_final: 0.8589 (m-40) REVERT: H 80 TYR cc_start: 0.8889 (m-80) cc_final: 0.8575 (m-80) REVERT: H 84 SER cc_start: 0.9172 (m) cc_final: 0.8668 (p) REVERT: K 14 LYS cc_start: 0.5407 (tppt) cc_final: 0.3637 (mmtt) REVERT: K 50 THR cc_start: 0.7485 (OUTLIER) cc_final: 0.7226 (m) REVERT: A 42 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.7259 (mmm-85) REVERT: A 79 LYS cc_start: 0.9020 (tttm) cc_final: 0.8630 (tttp) REVERT: A 108 ASN cc_start: 0.9172 (t0) cc_final: 0.8574 (t0) REVERT: A 120 MET cc_start: 0.8212 (mtp) cc_final: 0.7994 (mtp) REVERT: E 45 THR cc_start: 0.9260 (t) cc_final: 0.8834 (m) REVERT: E 63 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7941 (mmm-85) REVERT: E 105 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8389 (mm-30) outliers start: 43 outliers final: 33 residues processed: 285 average time/residue: 0.3406 time to fit residues: 130.0595 Evaluate side-chains 289 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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 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 68 ASN Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 45 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 50 THR Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR 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 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR 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 E residue 130 ILE 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 12 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 40.0000 chunk 96 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN A 39 HIS ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14550 Z= 0.369 Angle : 0.646 7.565 20935 Z= 0.371 Chirality : 0.039 0.151 2347 Planarity : 0.005 0.045 1614 Dihedral : 29.382 146.503 4323 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.21 % Allowed : 26.36 % Favored : 67.43 % 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: 0.45 (0.27), residues: 913 helix: 1.29 (0.22), residues: 547 sheet: -4.01 (0.97), residues: 20 loop : -1.02 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.016 0.002 HIS A 39 PHE 0.011 0.001 PHE H 67 TYR 0.057 0.002 TYR D 80 ARG 0.008 0.001 ARG E 40 *********************** 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 309 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 260 time to evaluate : 1.110 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: 0.8385 (mm-30) cc_final: 0.7969 (mm-30) REVERT: B 98 TYR cc_start: 0.9075 (m-10) cc_final: 0.8576 (m-10) REVERT: C 15 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8307 (mtmm) REVERT: C 36 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8626 (mmmm) REVERT: C 73 ASN cc_start: 0.8918 (t0) cc_final: 0.8179 (t0) REVERT: C 75 LYS cc_start: 0.9277 (mmtp) cc_final: 0.8976 (mmmm) REVERT: D 117 LYS cc_start: 0.9299 (tppp) cc_final: 0.8970 (ttmm) REVERT: F 35 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.8201 (ttt-90) REVERT: G 73 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8817 (t0) REVERT: G 75 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8954 (mttp) REVERT: G 90 ASP cc_start: 0.8351 (t70) cc_final: 0.8002 (t70) REVERT: H 64 ASN cc_start: 0.9052 (m-40) cc_final: 0.8714 (m-40) REVERT: H 80 TYR cc_start: 0.9013 (m-80) cc_final: 0.8387 (m-80) REVERT: H 84 SER cc_start: 0.9220 (m) cc_final: 0.8711 (p) REVERT: H 102 GLU cc_start: 0.7563 (tp30) cc_final: 0.6973 (tm-30) REVERT: K 14 LYS cc_start: 0.5486 (tppt) cc_final: 0.3736 (mptt) REVERT: K 50 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7247 (m) REVERT: A 42 ARG cc_start: 0.7766 (mmm-85) cc_final: 0.7443 (mmm-85) REVERT: A 79 LYS cc_start: 0.9077 (tttm) cc_final: 0.8586 (tttp) REVERT: A 120 MET cc_start: 0.8365 (mtp) cc_final: 0.7823 (mtp) REVERT: A 123 ASP cc_start: 0.8850 (m-30) cc_final: 0.8556 (m-30) REVERT: E 45 THR cc_start: 0.9334 (t) cc_final: 0.9088 (m) REVERT: E 54 TYR cc_start: 0.9097 (m-80) cc_final: 0.8557 (m-80) REVERT: E 105 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8332 (mm-30) outliers start: 49 outliers final: 39 residues processed: 280 average time/residue: 0.3248 time to fit residues: 122.3706 Evaluate side-chains 301 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 71 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 87 VAL 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 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 47 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 75 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 39 HIS 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 E residue 130 ILE 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 68 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 84 GLN G 73 ASN A 39 HIS E 39 HIS E 93 GLN E 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14550 Z= 0.225 Angle : 0.595 8.509 20935 Z= 0.344 Chirality : 0.036 0.148 2347 Planarity : 0.004 0.045 1614 Dihedral : 29.152 146.372 4323 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.45 % Allowed : 28.01 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.28), residues: 913 helix: 1.54 (0.23), residues: 546 sheet: -3.96 (0.95), residues: 20 loop : -0.98 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.014 0.001 HIS A 39 PHE 0.011 0.001 PHE E 67 TYR 0.052 0.002 TYR D 80 ARG 0.007 0.000 ARG G 71 *********************** 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 308 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 1.064 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: 0.8249 (mm-30) cc_final: 0.7960 (mm-30) REVERT: B 98 TYR cc_start: 0.9029 (m-10) cc_final: 0.8532 (m-10) REVERT: C 15 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7794 (mtmm) REVERT: C 73 ASN cc_start: 0.8932 (t0) cc_final: 0.8181 (t0) REVERT: C 75 LYS cc_start: 0.9269 (mmtp) cc_final: 0.8972 (mmmm) REVERT: D 91 ILE cc_start: 0.9038 (mm) cc_final: 0.8778 (mt) REVERT: D 105 LYS cc_start: 0.8515 (ptpp) cc_final: 0.8262 (pttm) REVERT: D 117 LYS cc_start: 0.9285 (tppp) cc_final: 0.8984 (ttmm) REVERT: F 25 ASN cc_start: 0.8347 (m-40) cc_final: 0.7970 (m-40) REVERT: F 84 MET cc_start: 0.7945 (mmm) cc_final: 0.7544 (mmm) REVERT: G 73 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8741 (t0) REVERT: G 90 ASP cc_start: 0.8294 (t70) cc_final: 0.7897 (t70) REVERT: G 110 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8677 (t0) REVERT: H 64 ASN cc_start: 0.8951 (m-40) cc_final: 0.8592 (m-40) REVERT: H 84 SER cc_start: 0.9221 (m) cc_final: 0.8718 (p) REVERT: K 14 LYS cc_start: 0.5439 (tppt) cc_final: 0.3726 (mmtt) REVERT: K 50 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.7120 (m) REVERT: A 42 ARG cc_start: 0.7721 (mmm-85) cc_final: 0.7420 (mmm-85) REVERT: A 79 LYS cc_start: 0.9065 (tttm) cc_final: 0.8584 (tttp) REVERT: A 108 ASN cc_start: 0.9157 (t0) cc_final: 0.8535 (t0) REVERT: A 120 MET cc_start: 0.8275 (mtp) cc_final: 0.7768 (mtp) REVERT: A 123 ASP cc_start: 0.8845 (m-30) cc_final: 0.8552 (m-30) REVERT: E 45 THR cc_start: 0.9302 (t) cc_final: 0.8926 (m) REVERT: E 105 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8258 (mm-30) outliers start: 43 outliers final: 32 residues processed: 285 average time/residue: 0.3155 time to fit residues: 122.0011 Evaluate side-chains 293 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 115 VAL 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 68 ASN 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 45 VAL Chi-restraints excluded: chain H residue 53 SER 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 50 THR 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 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 130 ILE 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 106 optimal weight: 0.2980 chunk 109 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN G 73 ASN A 39 HIS E 39 HIS E 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14550 Z= 0.243 Angle : 0.603 8.340 20935 Z= 0.348 Chirality : 0.036 0.178 2347 Planarity : 0.004 0.043 1614 Dihedral : 29.132 145.842 4323 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.58 % Allowed : 28.14 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 913 helix: 1.57 (0.23), residues: 549 sheet: -3.85 (0.96), residues: 20 loop : -0.97 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP L 21 HIS 0.010 0.001 HIS A 39 PHE 0.011 0.001 PHE E 67 TYR 0.054 0.002 TYR D 80 ARG 0.005 0.000 ARG G 71 *********************** 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 302 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 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: B 74 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7949 (mm-30) REVERT: B 92 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8496 (ttt-90) REVERT: B 98 TYR cc_start: 0.9018 (m-10) cc_final: 0.8519 (m-10) REVERT: C 15 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7835 (mtmm) REVERT: C 73 ASN cc_start: 0.8893 (t0) cc_final: 0.8186 (t0) REVERT: C 75 LYS cc_start: 0.9252 (mmtp) cc_final: 0.8954 (mmmm) REVERT: D 91 ILE cc_start: 0.9046 (mm) cc_final: 0.8794 (mt) REVERT: D 105 LYS cc_start: 0.8500 (ptpp) cc_final: 0.8233 (pttm) REVERT: D 117 LYS cc_start: 0.9287 (tppp) cc_final: 0.8996 (ttmm) REVERT: F 25 ASN cc_start: 0.8357 (m-40) cc_final: 0.7985 (m-40) REVERT: F 84 MET cc_start: 0.7824 (mmm) cc_final: 0.7110 (mmm) REVERT: G 73 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8713 (t0) REVERT: G 90 ASP cc_start: 0.8430 (t70) cc_final: 0.7927 (t0) REVERT: G 110 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8688 (t0) REVERT: H 64 ASN cc_start: 0.8957 (m-40) cc_final: 0.8601 (m-40) REVERT: H 80 TYR cc_start: 0.8851 (m-80) cc_final: 0.8237 (m-80) REVERT: H 84 SER cc_start: 0.9211 (m) cc_final: 0.8704 (p) REVERT: K 14 LYS cc_start: 0.5447 (tppt) cc_final: 0.3738 (mmtt) REVERT: K 50 THR cc_start: 0.7349 (OUTLIER) cc_final: 0.7102 (m) REVERT: A 42 ARG cc_start: 0.7726 (mmm-85) cc_final: 0.7452 (mmm-85) REVERT: A 79 LYS cc_start: 0.9078 (tttm) cc_final: 0.8666 (tttp) REVERT: A 120 MET cc_start: 0.8287 (mtp) cc_final: 0.7775 (mtp) REVERT: A 123 ASP cc_start: 0.8850 (m-30) cc_final: 0.8571 (m-30) REVERT: E 45 THR cc_start: 0.9271 (t) cc_final: 0.8922 (m) REVERT: E 63 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.8091 (mmm-85) REVERT: E 76 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8689 (tp-100) REVERT: E 105 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8290 (mm-30) outliers start: 44 outliers final: 35 residues processed: 278 average time/residue: 0.3221 time to fit residues: 121.1343 Evaluate side-chains 294 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR 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 115 VAL Chi-restraints excluded: chain D residue 120 SER 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 F residue 91 LYS Chi-restraints excluded: chain G residue 68 ASN 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 H residue 87 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 50 THR 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 87 SER Chi-restraints excluded: chain E residue 39 HIS 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 E residue 130 ILE 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 53 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 0.0670 chunk 28 optimal weight: 0.6980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN E 39 HIS E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14550 Z= 0.220 Angle : 0.601 8.896 20935 Z= 0.345 Chirality : 0.035 0.145 2347 Planarity : 0.004 0.045 1614 Dihedral : 29.083 145.513 4323 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.94 % Allowed : 28.77 % Favored : 66.29 % 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: 0.92 (0.28), residues: 913 helix: 1.72 (0.23), residues: 547 sheet: -3.81 (0.97), residues: 20 loop : -0.93 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP L 21 HIS 0.007 0.001 HIS A 39 PHE 0.011 0.001 PHE E 67 TYR 0.051 0.002 TYR D 80 ARG 0.009 0.001 ARG E 40 ********************** 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 292 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 1.111 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: 0.8243 (mm-30) cc_final: 0.7945 (mm-30) REVERT: B 92 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8510 (ttt-90) REVERT: B 98 TYR cc_start: 0.9014 (m-10) cc_final: 0.8520 (m-10) REVERT: C 15 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7798 (mtmm) REVERT: C 73 ASN cc_start: 0.8842 (t0) cc_final: 0.8162 (t0) REVERT: C 75 LYS cc_start: 0.9236 (mmtp) cc_final: 0.8939 (mmmm) REVERT: D 91 ILE cc_start: 0.9034 (mm) cc_final: 0.8778 (mt) REVERT: D 105 LYS cc_start: 0.8496 (ptpp) cc_final: 0.8214 (pttm) REVERT: D 117 LYS cc_start: 0.9295 (tppp) cc_final: 0.9007 (ttmm) REVERT: F 25 ASN cc_start: 0.8344 (m-40) cc_final: 0.8015 (m-40) REVERT: F 35 ARG cc_start: 0.8571 (ttt90) cc_final: 0.7875 (tpt-90) REVERT: F 84 MET cc_start: 0.7806 (mmm) cc_final: 0.7122 (mmm) REVERT: G 73 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8779 (t0) REVERT: G 90 ASP cc_start: 0.8325 (t70) cc_final: 0.7884 (t0) REVERT: G 110 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8677 (t0) REVERT: H 64 ASN cc_start: 0.8940 (m-40) cc_final: 0.8554 (m-40) REVERT: H 80 TYR cc_start: 0.8823 (m-80) cc_final: 0.8205 (m-80) REVERT: H 84 SER cc_start: 0.9223 (m) cc_final: 0.8751 (p) REVERT: H 102 GLU cc_start: 0.7435 (tp30) cc_final: 0.7154 (tm-30) REVERT: H 117 LYS cc_start: 0.9026 (tppp) cc_final: 0.8813 (ttpp) REVERT: K 14 LYS cc_start: 0.5427 (tppt) cc_final: 0.3745 (mmtt) REVERT: K 50 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.7076 (m) REVERT: A 79 LYS cc_start: 0.9075 (tttm) cc_final: 0.8664 (tttp) REVERT: A 120 MET cc_start: 0.8254 (mtp) cc_final: 0.8031 (mtp) REVERT: E 41 TYR cc_start: 0.8795 (m-10) cc_final: 0.8592 (m-10) REVERT: E 45 THR cc_start: 0.9251 (t) cc_final: 0.8926 (m) REVERT: E 76 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8663 (tp-100) REVERT: E 105 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8335 (mm-30) outliers start: 39 outliers final: 33 residues processed: 270 average time/residue: 0.3160 time to fit residues: 115.3920 Evaluate side-chains 289 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 92 ARG 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 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 120 SER 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 F residue 91 LYS Chi-restraints excluded: chain G residue 68 ASN 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 87 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 50 THR 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 39 HIS 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 E residue 130 ILE 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 87 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN E 39 HIS E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.154903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089795 restraints weight = 21719.148| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.73 r_work: 0.2845 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14550 Z= 0.234 Angle : 0.602 8.521 20935 Z= 0.345 Chirality : 0.036 0.142 2347 Planarity : 0.004 0.045 1614 Dihedral : 29.075 145.095 4323 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.07 % Allowed : 28.52 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.28), residues: 913 helix: 1.81 (0.23), residues: 545 sheet: -3.75 (0.97), residues: 20 loop : -0.93 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 21 HIS 0.005 0.001 HIS E 39 PHE 0.011 0.001 PHE E 67 TYR 0.051 0.002 TYR D 80 ARG 0.008 0.001 ARG G 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.54 seconds wall clock time: 58 minutes 51.99 seconds (3531.99 seconds total)