Starting phenix.real_space_refine on Sat Mar 16 07:02:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smw_40604/03_2024/8smw_40604.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smw_40604/03_2024/8smw_40604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smw_40604/03_2024/8smw_40604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smw_40604/03_2024/8smw_40604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smw_40604/03_2024/8smw_40604.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smw_40604/03_2024/8smw_40604.pdb" } resolution = 3.3 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= 0.000 sd= 0.105 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 32 5.16 5 C 7891 2.51 5 N 2608 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "L PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13998 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 34.563 67.474 43.721 1.00 33.88 S ATOM 12446 SG CYS K 51 32.713 64.181 43.621 1.00 29.69 S ATOM 12470 SG CYS K 54 34.556 65.439 40.531 1.00 35.60 S ATOM 12187 SG CYS K 16 22.929 63.352 48.998 1.00 58.51 S ATOM 12205 SG CYS K 19 20.440 61.444 50.962 1.00 60.46 S ATOM 12335 SG CYS K 36 23.193 63.501 52.800 1.00 47.61 S ATOM 12357 SG CYS K 39 24.103 60.352 51.278 1.00 48.10 S Time building chain proxies: 8.08, per 1000 atoms: 0.58 Number of scatterers: 13998 At special positions: 0 Unit cell: (108.896, 130.144, 128.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 32 16.00 P 294 15.00 O 3171 8.00 N 2608 7.00 C 7891 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 - 3.50 Amino acid : False - 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: 7.06 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 64.2% alpha, 4.5% beta 136 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 6.49 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.615A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.783A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.043A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.504A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.553A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.749A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.692A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 4.069A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.690A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.851A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.618A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.579A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.571A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.549A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.760A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 67 removed outlier: 3.841A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 3.661A pdb=" N TRP K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 4.377A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS K 89 " --> pdb=" O PRO K 85 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.811A pdb=" N ARG L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.568A pdb=" N LEU L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 Processing helix chain 'L' and resid 130 through 146 removed outlier: 3.548A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS L 144 " --> pdb=" O GLU L 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.940A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.625A 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: 7.542A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 101 through 102 removed outlier: 6.860A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.101A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.714A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (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 removed outlier: 3.536A pdb=" N ILE G 78 " --> pdb=" O GLY H 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25 464 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 7.53 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: 2994 1.33 - 1.46: 4511 1.46 - 1.58: 6726 1.58 - 1.70: 586 1.70 - 1.82: 47 Bond restraints: 14864 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CG PRO L 61 " pdb=" CD PRO L 61 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.70e-02 1.37e+03 1.15e+00 bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.45e-01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.88e-01 ... (remaining 14859 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.73: 1608 105.73 - 112.81: 8204 112.81 - 119.88: 5173 119.88 - 126.95: 5604 126.95 - 134.03: 764 Bond angle restraints: 21353 Sorted by residual: angle pdb=" CB MET L 30 " pdb=" CG MET L 30 " pdb=" SD MET L 30 " ideal model delta sigma weight residual 112.70 121.16 -8.46 3.00e+00 1.11e-01 7.96e+00 angle pdb=" C3' DG J -70 " pdb=" C2' DG J -70 " pdb=" C1' DG J -70 " ideal model delta sigma weight residual 101.60 105.42 -3.82 1.50e+00 4.44e-01 6.47e+00 angle pdb=" C ALA D 110 " pdb=" N VAL D 111 " pdb=" CA VAL D 111 " ideal model delta sigma weight residual 120.60 123.59 -2.99 1.29e+00 6.01e-01 5.38e+00 angle pdb=" N ASN G 73 " pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 112.59 109.81 2.78 1.22e+00 6.72e-01 5.20e+00 angle pdb=" N ASN L 7 " pdb=" CA ASN L 7 " pdb=" CB ASN L 7 " ideal model delta sigma weight residual 110.12 113.41 -3.29 1.47e+00 4.63e-01 5.00e+00 ... (remaining 21348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 6852 35.68 - 71.37: 1353 71.37 - 107.05: 17 107.05 - 142.74: 0 142.74 - 178.42: 2 Dihedral angle restraints: 8224 sinusoidal: 5302 harmonic: 2922 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.42 -178.42 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 71.12 148.88 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" CG ARG F 67 " pdb=" CD ARG F 67 " pdb=" NE ARG F 67 " pdb=" CZ ARG F 67 " ideal model delta sinusoidal sigma weight residual 90.00 134.35 -44.35 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 8221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1541 0.026 - 0.052: 591 0.052 - 0.078: 195 0.078 - 0.105: 62 0.105 - 0.131: 30 Chirality restraints: 2419 Sorted by residual: chirality pdb=" CA VAL K 24 " pdb=" N VAL K 24 " pdb=" C VAL K 24 " pdb=" CB VAL K 24 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CB ILE K 8 " pdb=" CA ILE K 8 " pdb=" CG1 ILE K 8 " pdb=" CG2 ILE K 8 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 2416 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.026 2.00e-02 2.50e+03 1.13e-02 3.50e+00 pdb=" N9 DA I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.022 2.00e-02 2.50e+03 9.01e-03 2.44e+00 pdb=" N9 DG I 47 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 107 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ALA D 107 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA D 107 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS D 108 " -0.008 2.00e-02 2.50e+03 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1796 2.76 - 3.47: 17701 3.47 - 4.19: 37398 4.19 - 4.90: 58585 Nonbonded interactions: 115482 Sorted by model distance: nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.329 3.350 nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.331 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.124 2.496 nonbonded pdb=" O ASN G 73 " pdb=" ND2 ASN G 73 " model vdw 2.244 2.520 nonbonded pdb=" N SER C 11 " pdb=" O SER D 123 " model vdw 2.250 2.520 ... (remaining 115477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.440 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 47.740 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.003 0.036 14864 Z= 0.180 Angle : 0.529 8.463 21353 Z= 0.315 Chirality : 0.034 0.131 2419 Planarity : 0.004 0.035 1688 Dihedral : 26.233 178.423 6336 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.72 (0.27), residues: 983 helix: 2.18 (0.21), residues: 625 sheet: 0.52 (1.01), residues: 24 loop : -0.86 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 61 HIS 0.003 0.001 HIS L 0 PHE 0.009 0.001 PHE L 62 TYR 0.009 0.001 TYR F 51 ARG 0.007 0.000 ARG L 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.115 Fit side-chains REVERT: C 73 ASN cc_start: 0.7713 (m-40) cc_final: 0.7270 (t0) REVERT: D 99 ARG cc_start: 0.7840 (mtt-85) cc_final: 0.7445 (mtm-85) REVERT: H 46 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8435 (mmtt) REVERT: H 79 ARG cc_start: 0.8895 (ttm110) cc_final: 0.8512 (ttm170) REVERT: H 99 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7496 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3995 time to fit residues: 57.8324 Evaluate side-chains 98 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.0570 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN L 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14864 Z= 0.179 Angle : 0.533 7.357 21353 Z= 0.316 Chirality : 0.034 0.137 2419 Planarity : 0.004 0.032 1688 Dihedral : 29.264 178.352 4332 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.70 % Allowed : 4.56 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.97 (0.27), residues: 983 helix: 2.37 (0.21), residues: 633 sheet: 0.53 (1.01), residues: 24 loop : -0.84 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 61 HIS 0.002 0.001 HIS H 82 PHE 0.009 0.001 PHE L 50 TYR 0.008 0.001 TYR F 51 ARG 0.003 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.117 Fit side-chains REVERT: C 73 ASN cc_start: 0.7601 (m-40) cc_final: 0.7095 (t0) REVERT: D 99 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7486 (mtm-85) REVERT: H 46 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8418 (mmtt) REVERT: H 99 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7548 (mtm180) REVERT: L 30 MET cc_start: 0.6055 (mmm) cc_final: 0.5850 (mmm) REVERT: L 137 ILE cc_start: 0.6675 (tp) cc_final: 0.6462 (tp) REVERT: L 147 MET cc_start: 0.5950 (OUTLIER) cc_final: 0.5664 (ptp) outliers start: 6 outliers final: 4 residues processed: 105 average time/residue: 0.3641 time to fit residues: 50.9433 Evaluate side-chains 107 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 147 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.0030 chunk 119 optimal weight: 0.0770 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 overall best weight: 0.7550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN L 7 ASN L 92 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14864 Z= 0.183 Angle : 0.516 5.678 21353 Z= 0.308 Chirality : 0.034 0.126 2419 Planarity : 0.004 0.036 1688 Dihedral : 29.055 178.345 4332 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.93 % Allowed : 6.89 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.17 (0.27), residues: 983 helix: 2.55 (0.21), residues: 634 sheet: 0.61 (1.04), residues: 24 loop : -0.82 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 61 HIS 0.002 0.001 HIS H 49 PHE 0.009 0.001 PHE L 62 TYR 0.007 0.001 TYR F 51 ARG 0.002 0.000 ARG L 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.188 Fit side-chains REVERT: C 73 ASN cc_start: 0.7429 (m-40) cc_final: 0.7073 (t0) REVERT: D 99 ARG cc_start: 0.7822 (mtt-85) cc_final: 0.7436 (mtm-85) REVERT: H 99 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7562 (mtm180) REVERT: L 7 ASN cc_start: 0.8660 (m-40) cc_final: 0.8305 (m110) REVERT: L 30 MET cc_start: 0.5883 (mmm) cc_final: 0.5612 (mmm) REVERT: L 137 ILE cc_start: 0.6740 (tp) cc_final: 0.6523 (tp) outliers start: 8 outliers final: 4 residues processed: 108 average time/residue: 0.3511 time to fit residues: 51.3284 Evaluate side-chains 100 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14864 Z= 0.266 Angle : 0.557 5.674 21353 Z= 0.327 Chirality : 0.037 0.134 2419 Planarity : 0.004 0.034 1688 Dihedral : 29.437 178.154 4332 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.17 % Allowed : 7.94 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.94 (0.27), residues: 983 helix: 2.43 (0.21), residues: 632 sheet: 0.63 (1.05), residues: 24 loop : -1.03 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 61 HIS 0.004 0.001 HIS H 49 PHE 0.012 0.002 PHE D 65 TYR 0.011 0.002 TYR F 51 ARG 0.004 0.000 ARG L 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.159 Fit side-chains REVERT: C 73 ASN cc_start: 0.7647 (m-40) cc_final: 0.7299 (t0) REVERT: D 99 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7637 (mtm-85) REVERT: D 113 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8079 (mm-30) REVERT: H 46 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8458 (mmtt) REVERT: H 99 ARG cc_start: 0.7982 (mtt-85) cc_final: 0.7552 (mtm-85) REVERT: L 7 ASN cc_start: 0.8671 (m-40) cc_final: 0.8151 (m110) REVERT: L 30 MET cc_start: 0.6090 (mmm) cc_final: 0.5792 (mmm) outliers start: 10 outliers final: 8 residues processed: 98 average time/residue: 0.3689 time to fit residues: 48.5574 Evaluate side-chains 95 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14864 Z= 0.214 Angle : 0.526 6.907 21353 Z= 0.312 Chirality : 0.035 0.132 2419 Planarity : 0.004 0.035 1688 Dihedral : 29.290 178.578 4332 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.82 % Allowed : 9.00 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.98 (0.27), residues: 983 helix: 2.45 (0.21), residues: 634 sheet: 0.50 (1.04), residues: 24 loop : -1.01 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 61 HIS 0.003 0.001 HIS H 49 PHE 0.009 0.001 PHE D 65 TYR 0.008 0.001 TYR F 51 ARG 0.002 0.000 ARG L 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 1.151 Fit side-chains REVERT: C 73 ASN cc_start: 0.7458 (m-40) cc_final: 0.7195 (t0) REVERT: D 99 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.7560 (mtm-85) REVERT: D 113 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8006 (mm-30) REVERT: H 46 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8457 (mmtt) REVERT: K 46 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8592 (ttmm) REVERT: L 30 MET cc_start: 0.6087 (mmm) cc_final: 0.5824 (mmm) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.3853 time to fit residues: 48.8811 Evaluate side-chains 97 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14864 Z= 0.165 Angle : 0.515 6.191 21353 Z= 0.307 Chirality : 0.034 0.131 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.253 178.705 4332 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.05 % Allowed : 9.93 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.07 (0.27), residues: 983 helix: 2.53 (0.21), residues: 634 sheet: 0.58 (1.05), residues: 24 loop : -1.00 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 61 HIS 0.002 0.001 HIS H 49 PHE 0.009 0.001 PHE L 62 TYR 0.008 0.001 TYR F 51 ARG 0.001 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.099 Fit side-chains REVERT: C 73 ASN cc_start: 0.7412 (m-40) cc_final: 0.7169 (t0) REVERT: D 99 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7562 (mtm-85) REVERT: D 113 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7975 (mm-30) REVERT: H 46 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8451 (mmtt) REVERT: H 99 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7642 (mtm-85) REVERT: L 30 MET cc_start: 0.6071 (mmm) cc_final: 0.5802 (mmm) outliers start: 9 outliers final: 5 residues processed: 93 average time/residue: 0.3744 time to fit residues: 46.4947 Evaluate side-chains 94 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14864 Z= 0.330 Angle : 0.589 8.175 21353 Z= 0.342 Chirality : 0.038 0.134 2419 Planarity : 0.004 0.037 1688 Dihedral : 29.597 178.096 4332 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.05 % Allowed : 10.28 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.67 (0.27), residues: 983 helix: 2.26 (0.21), residues: 631 sheet: 0.61 (1.04), residues: 24 loop : -1.24 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 61 HIS 0.005 0.001 HIS H 49 PHE 0.014 0.002 PHE A 78 TYR 0.011 0.002 TYR F 51 ARG 0.003 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.170 Fit side-chains REVERT: C 73 ASN cc_start: 0.7763 (m-40) cc_final: 0.7359 (t0) REVERT: D 99 ARG cc_start: 0.7937 (mtt-85) cc_final: 0.7650 (mtm-85) REVERT: D 113 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8085 (mm-30) REVERT: H 46 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8417 (mmtt) REVERT: K 46 LYS cc_start: 0.8894 (ttmt) cc_final: 0.8643 (ttmm) REVERT: L 30 MET cc_start: 0.6188 (mmm) cc_final: 0.5860 (mmm) outliers start: 9 outliers final: 8 residues processed: 97 average time/residue: 0.3753 time to fit residues: 48.3033 Evaluate side-chains 96 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14864 Z= 0.175 Angle : 0.535 8.454 21353 Z= 0.318 Chirality : 0.035 0.139 2419 Planarity : 0.004 0.059 1688 Dihedral : 29.421 178.826 4332 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.82 % Allowed : 11.45 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.90 (0.27), residues: 983 helix: 2.44 (0.21), residues: 632 sheet: 0.70 (1.06), residues: 24 loop : -1.15 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 61 HIS 0.002 0.001 HIS A 39 PHE 0.010 0.001 PHE L 50 TYR 0.008 0.001 TYR G 50 ARG 0.008 0.000 ARG K 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.197 Fit side-chains REVERT: C 73 ASN cc_start: 0.7555 (m-40) cc_final: 0.7238 (t0) REVERT: D 99 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7563 (mtm-85) REVERT: D 113 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8000 (mm-30) REVERT: H 46 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8370 (mmtt) REVERT: K 46 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8652 (ttmm) REVERT: L 30 MET cc_start: 0.6152 (mmm) cc_final: 0.5860 (mmm) outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 0.3846 time to fit residues: 48.0034 Evaluate side-chains 93 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 115 optimal weight: 10.0000 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14864 Z= 0.211 Angle : 0.529 8.630 21353 Z= 0.313 Chirality : 0.035 0.134 2419 Planarity : 0.004 0.036 1688 Dihedral : 29.291 178.740 4332 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.17 % Allowed : 11.33 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.91 (0.27), residues: 983 helix: 2.44 (0.21), residues: 632 sheet: 0.69 (1.06), residues: 24 loop : -1.14 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 61 HIS 0.003 0.001 HIS H 49 PHE 0.009 0.001 PHE D 65 TYR 0.009 0.001 TYR F 51 ARG 0.007 0.000 ARG K 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.142 Fit side-chains REVERT: A 59 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7991 (pm20) REVERT: C 73 ASN cc_start: 0.7444 (m-40) cc_final: 0.7221 (t0) REVERT: D 99 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7577 (mtm-85) REVERT: D 113 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8074 (mm-30) REVERT: H 46 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8442 (mmtt) REVERT: K 46 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8578 (ttmm) REVERT: L 30 MET cc_start: 0.6161 (mmm) cc_final: 0.5869 (mmm) outliers start: 10 outliers final: 7 residues processed: 97 average time/residue: 0.3602 time to fit residues: 46.7099 Evaluate side-chains 97 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14864 Z= 0.211 Angle : 0.533 9.407 21353 Z= 0.314 Chirality : 0.035 0.133 2419 Planarity : 0.004 0.036 1688 Dihedral : 29.284 178.782 4332 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.05 % Allowed : 11.45 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.89 (0.27), residues: 983 helix: 2.42 (0.21), residues: 632 sheet: 0.75 (1.06), residues: 24 loop : -1.14 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 61 HIS 0.003 0.001 HIS H 49 PHE 0.011 0.002 PHE L 50 TYR 0.009 0.001 TYR F 51 ARG 0.008 0.000 ARG K 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 1.071 Fit side-chains REVERT: A 59 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7990 (pm20) REVERT: C 73 ASN cc_start: 0.7446 (m-40) cc_final: 0.7223 (t0) REVERT: D 99 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7578 (mtm-85) REVERT: D 113 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8069 (mm-30) REVERT: H 46 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8459 (mmtt) REVERT: K 46 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8615 (ttmm) REVERT: L 30 MET cc_start: 0.6162 (mmm) cc_final: 0.5868 (mmm) outliers start: 9 outliers final: 8 residues processed: 93 average time/residue: 0.3837 time to fit residues: 47.5252 Evaluate side-chains 97 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 147 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.0000 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.153858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.097446 restraints weight = 24621.025| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.84 r_work: 0.2652 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14864 Z= 0.219 Angle : 0.535 9.592 21353 Z= 0.315 Chirality : 0.035 0.134 2419 Planarity : 0.004 0.036 1688 Dihedral : 29.286 178.721 4332 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.93 % Allowed : 11.45 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.87 (0.27), residues: 983 helix: 2.41 (0.21), residues: 632 sheet: 0.77 (1.06), residues: 24 loop : -1.16 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 61 HIS 0.003 0.001 HIS H 49 PHE 0.010 0.002 PHE D 65 TYR 0.009 0.001 TYR F 51 ARG 0.008 0.000 ARG K 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2388.19 seconds wall clock time: 43 minutes 48.38 seconds (2628.38 seconds total)