Starting phenix.real_space_refine on Mon May 19 11:22:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8upf_42446/05_2025/8upf_42446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8upf_42446/05_2025/8upf_42446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8upf_42446/05_2025/8upf_42446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8upf_42446/05_2025/8upf_42446.map" model { file = "/net/cci-nas-00/data/ceres_data/8upf_42446/05_2025/8upf_42446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8upf_42446/05_2025/8upf_42446.cif" } resolution = 3.2 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= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. 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 293 5.49 5 S 32 5.16 5 C 7901 2.51 5 N 2612 2.21 5 O 3172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14012 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: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} 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: "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: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 706 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Conformer: "B" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} bond proxies already assigned to first conformer: 713 Chain: "L" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1175 Classifications: {'peptide': 148} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "C" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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 10623 SG CYS K 31 73.925 71.146 46.276 1.00186.03 S ATOM 10773 SG CYS K 51 75.294 73.936 47.616 1.00186.41 S ATOM 10797 SG CYS K 54 74.227 74.593 43.507 1.00191.01 S ATOM 10514 SG CYS K 16 82.497 72.048 55.513 1.00233.53 S ATOM 10532 SG CYS K 19 84.522 73.207 59.045 1.00237.17 S ATOM 10662 SG CYS K 36 81.475 70.277 59.358 1.00213.12 S ATOM 10684 SG CYS K 39 81.052 73.736 58.594 1.00206.20 S Time building chain proxies: 8.47, per 1000 atoms: 0.60 Number of scatterers: 14012 At special positions: 0 Unit cell: (105.843, 127.422, 116.119, 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 293 15.00 O 3172 8.00 N 2612 7.00 C 7901 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 64.8% alpha, 4.3% beta 135 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.575A 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 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.872A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.519A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.679A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.828A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.575A 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: 3.916A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 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: 3.802A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.544A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 46 Processing helix chain 'K' and resid 58 through 67 Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 93 removed outlier: 3.630A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) Processing helix chain 'L' and resid -1 through 16 Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.666A pdb=" N VAL L 102 " --> pdb=" O THR L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.544A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.568A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.708A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.456A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.237A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.629A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.411A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 removed outlier: 3.590A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25 481 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 3.78 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: 3005 1.33 - 1.45: 4434 1.45 - 1.57: 6805 1.57 - 1.69: 584 1.69 - 1.81: 46 Bond restraints: 14874 Sorted by residual: bond pdb=" CA ALA F 76 " pdb=" C ALA F 76 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.72e-02 3.38e+03 3.68e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.50e+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 1.32e+00 bond pdb=" C4' DC J -26 " pdb=" C3' DC J -26 " ideal model delta sigma weight residual 1.523 1.500 0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" C4' DG I 9 " pdb=" C3' DG I 9 " ideal model delta sigma weight residual 1.523 1.500 0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 14869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 20154 1.30 - 2.61: 1091 2.61 - 3.91: 82 3.91 - 5.21: 21 5.21 - 6.52: 10 Bond angle restraints: 21358 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 122.46 126.18 -3.72 1.41e+00 5.03e-01 6.96e+00 angle pdb=" C3' DT J 66 " pdb=" C2' DT J 66 " pdb=" C1' DT J 66 " ideal model delta sigma weight residual 101.60 97.80 3.80 1.50e+00 4.44e-01 6.43e+00 angle pdb=" C3' DT J -29 " pdb=" C2' DT J -29 " pdb=" C1' DT J -29 " ideal model delta sigma weight residual 101.60 97.87 3.73 1.50e+00 4.44e-01 6.19e+00 angle pdb=" N LYS E 37 " pdb=" CA LYS E 37 " pdb=" C LYS E 37 " ideal model delta sigma weight residual 111.00 117.52 -6.52 2.80e+00 1.28e-01 5.42e+00 angle pdb=" N LYS A 37 " pdb=" CA LYS A 37 " pdb=" C LYS A 37 " ideal model delta sigma weight residual 111.00 117.51 -6.51 2.80e+00 1.28e-01 5.41e+00 ... (remaining 21353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 6572 31.32 - 62.63: 1618 62.63 - 93.95: 47 93.95 - 125.27: 0 125.27 - 156.58: 2 Dihedral angle restraints: 8239 sinusoidal: 5301 harmonic: 2938 Sorted by residual: 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 63.42 156.58 1 3.50e+01 8.16e-04 1.50e+01 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 220.00 65.18 154.82 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA HIS H 49 " pdb=" C HIS H 49 " pdb=" N PRO H 50 " pdb=" CA PRO H 50 " ideal model delta harmonic sigma weight residual -180.00 -162.73 -17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 8236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1533 0.033 - 0.067: 702 0.067 - 0.100: 133 0.100 - 0.133: 44 0.133 - 0.167: 8 Chirality restraints: 2420 Sorted by residual: chirality pdb=" CA LYS E 37 " pdb=" N LYS E 37 " pdb=" C LYS E 37 " pdb=" CB LYS E 37 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA LYS A 37 " pdb=" N LYS A 37 " pdb=" C LYS A 37 " pdb=" CB LYS A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 2417 not shown) Planarity restraints: 1693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.029 2.00e-02 2.50e+03 1.19e-02 4.28e+00 pdb=" N9 DG I 47 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.000 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 " -0.004 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=" C1' DA I -5 " -0.028 2.00e-02 2.50e+03 1.24e-02 4.22e+00 pdb=" N9 DA I -5 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA I -5 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -5 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DA I -5 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -5 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I -5 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -5 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -5 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -5 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I -5 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO B 32 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.026 5.00e-02 4.00e+02 ... (remaining 1690 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 195 2.63 - 3.20: 12339 3.20 - 3.77: 25525 3.77 - 4.33: 33601 4.33 - 4.90: 48902 Nonbonded interactions: 120562 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.065 2.496 nonbonded pdb=" OG SER D 78 " pdb=" O TYR C 39 " model vdw 2.141 3.040 nonbonded pdb=" O ARG L 125 " pdb=" OG1 THR L 129 " model vdw 2.163 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.216 3.040 ... (remaining 120557 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' 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 119) } 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 39.240 Find NCS groups from input model: 0.330 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 0.283 14884 Z= 0.318 Angle : 0.735 27.209 21373 Z= 0.395 Chirality : 0.039 0.167 2420 Planarity : 0.004 0.046 1691 Dihedral : 26.919 156.584 6337 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.47 % Allowed : 5.00 % Favored : 94.53 % 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: -2.24 (0.24), residues: 989 helix: -0.85 (0.18), residues: 647 sheet: -1.85 (0.94), residues: 23 loop : -2.60 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 61 HIS 0.004 0.001 HIS L 75 PHE 0.011 0.001 PHE E 78 TYR 0.013 0.002 TYR C 50 ARG 0.003 0.000 ARG L 136 Details of bonding type rmsd link_TRANS : bond 0.00050 ( 2) link_TRANS : angle 0.74427 ( 6) hydrogen bonds : bond 0.10676 ( 828) hydrogen bonds : angle 5.05605 ( 2106) metal coordination : bond 0.15181 ( 8) metal coordination : angle 16.71906 ( 9) covalent geometry : bond 0.00692 (14874) covalent geometry : angle 0.64995 (21358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9188 (m-80) cc_final: 0.8895 (m-80) REVERT: A 59 GLU cc_start: 0.8466 (pm20) cc_final: 0.8160 (pm20) REVERT: A 60 LEU cc_start: 0.9166 (mt) cc_final: 0.8852 (mt) REVERT: A 80 THR cc_start: 0.8601 (t) cc_final: 0.8045 (t) REVERT: B 92 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8347 (ttp80) REVERT: D 59 MET cc_start: 0.8950 (tpp) cc_final: 0.7857 (tpt) REVERT: D 83 TYR cc_start: 0.8630 (m-10) cc_final: 0.8335 (m-10) REVERT: D 108 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7484 (mtpp) REVERT: E 50 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7417 (mt-10) REVERT: F 25 ASN cc_start: 0.8460 (m110) cc_final: 0.7918 (m-40) REVERT: F 91 LYS cc_start: 0.9099 (ttmt) cc_final: 0.8768 (ttpp) REVERT: H 86 ARG cc_start: 0.8808 (mmt-90) cc_final: 0.8579 (ttm-80) REVERT: H 113 GLU cc_start: 0.8517 (tp30) cc_final: 0.8249 (tm-30) REVERT: H 120 LYS cc_start: 0.8475 (tttm) cc_final: 0.8222 (tttt) REVERT: K 20 MET cc_start: 0.7240 (mmp) cc_final: 0.6847 (mpp) REVERT: L 30 MET cc_start: 0.6403 (ptt) cc_final: 0.6106 (mmm) REVERT: C 104 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8731 (tp40) REVERT: G 36 LYS cc_start: 0.8543 (pttt) cc_final: 0.8029 (mmmm) REVERT: G 104 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8464 (mm-40) outliers start: 4 outliers final: 0 residues processed: 176 average time/residue: 0.4045 time to fit residues: 91.0534 Evaluate side-chains 156 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 93 optimal weight: 40.0000 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN K 41 GLN K 81 GLN K 83 HIS L 77 ASN C 112 GLN G 38 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.138538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.081298 restraints weight = 34244.455| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.86 r_work: 0.2820 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14884 Z= 0.219 Angle : 0.611 9.429 21373 Z= 0.348 Chirality : 0.037 0.161 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.879 156.436 4324 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.93 % Allowed : 11.28 % Favored : 87.79 % 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: -0.18 (0.26), residues: 989 helix: 0.78 (0.20), residues: 657 sheet: -1.26 (1.04), residues: 23 loop : -1.96 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 PHE 0.011 0.002 PHE L 62 TYR 0.025 0.002 TYR H 121 ARG 0.004 0.000 ARG E 134 Details of bonding type rmsd link_TRANS : bond 0.00263 ( 2) link_TRANS : angle 0.37609 ( 6) hydrogen bonds : bond 0.04461 ( 828) hydrogen bonds : angle 3.45636 ( 2106) metal coordination : bond 0.02348 ( 8) metal coordination : angle 4.81147 ( 9) covalent geometry : bond 0.00505 (14874) covalent geometry : angle 0.60315 (21358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8368 (pm20) cc_final: 0.8067 (pm20) REVERT: B 84 MET cc_start: 0.8960 (mmm) cc_final: 0.8346 (mmm) REVERT: D 68 ASP cc_start: 0.9117 (t70) cc_final: 0.8809 (t0) REVERT: D 108 LYS cc_start: 0.7612 (ttpt) cc_final: 0.7372 (mtpp) REVERT: F 25 ASN cc_start: 0.8487 (m110) cc_final: 0.7944 (m-40) REVERT: F 91 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8754 (ttpp) REVERT: H 113 GLU cc_start: 0.8648 (tp30) cc_final: 0.7673 (tm-30) REVERT: K 20 MET cc_start: 0.7052 (mmp) cc_final: 0.6796 (mpp) REVERT: C 24 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8694 (mm-40) REVERT: C 61 GLU cc_start: 0.8626 (tp30) cc_final: 0.8115 (tt0) REVERT: C 92 GLU cc_start: 0.8354 (mp0) cc_final: 0.8048 (mp0) REVERT: C 104 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8852 (tp40) REVERT: G 36 LYS cc_start: 0.8238 (pttt) cc_final: 0.7704 (mmtp) REVERT: G 92 GLU cc_start: 0.8550 (mp0) cc_final: 0.7626 (mp0) REVERT: G 104 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8829 (mm110) outliers start: 8 outliers final: 4 residues processed: 156 average time/residue: 0.3721 time to fit residues: 76.9171 Evaluate side-chains 138 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 99 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 30.0000 chunk 119 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 96 optimal weight: 0.0570 chunk 6 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN F 27 GLN F 93 GLN H 84 ASN K 81 GLN G 38 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.143773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.086793 restraints weight = 40506.442| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.14 r_work: 0.2900 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14884 Z= 0.140 Angle : 0.553 6.997 21373 Z= 0.321 Chirality : 0.034 0.156 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.219 158.642 4324 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.28 % Allowed : 14.19 % Favored : 84.53 % 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: 1.09 (0.27), residues: 989 helix: 1.81 (0.20), residues: 657 sheet: -0.32 (1.16), residues: 23 loop : -1.66 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 77 HIS 0.006 0.001 HIS K 65 PHE 0.008 0.001 PHE L 69 TYR 0.024 0.001 TYR H 121 ARG 0.004 0.000 ARG E 134 Details of bonding type rmsd link_TRANS : bond 0.00091 ( 2) link_TRANS : angle 0.34616 ( 6) hydrogen bonds : bond 0.03691 ( 828) hydrogen bonds : angle 2.92728 ( 2106) metal coordination : bond 0.01572 ( 8) metal coordination : angle 3.37124 ( 9) covalent geometry : bond 0.00296 (14874) covalent geometry : angle 0.54848 (21358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8134 (pm20) cc_final: 0.7769 (pm20) REVERT: B 84 MET cc_start: 0.8819 (mmm) cc_final: 0.8290 (mmm) REVERT: B 98 TYR cc_start: 0.9287 (m-10) cc_final: 0.8988 (m-10) REVERT: D 68 ASP cc_start: 0.8989 (t70) cc_final: 0.8711 (t0) REVERT: D 83 TYR cc_start: 0.8686 (m-10) cc_final: 0.8325 (m-80) REVERT: D 87 SER cc_start: 0.8804 (m) cc_final: 0.8297 (p) REVERT: F 25 ASN cc_start: 0.8498 (m110) cc_final: 0.7939 (m-40) REVERT: F 91 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8724 (ttpp) REVERT: H 86 ARG cc_start: 0.8516 (mmt-90) cc_final: 0.8300 (ttm-80) REVERT: H 113 GLU cc_start: 0.8556 (tp30) cc_final: 0.8157 (tm-30) REVERT: K 20 MET cc_start: 0.7073 (mmp) cc_final: 0.6720 (mpp) REVERT: L 30 MET cc_start: 0.6072 (mmm) cc_final: 0.5779 (ptt) REVERT: C 92 GLU cc_start: 0.8439 (mp0) cc_final: 0.8010 (mp0) REVERT: C 104 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8810 (tp40) REVERT: G 36 LYS cc_start: 0.8183 (pttt) cc_final: 0.7722 (mmtp) REVERT: G 72 ASP cc_start: 0.8891 (m-30) cc_final: 0.8497 (m-30) REVERT: G 92 GLU cc_start: 0.8584 (mp0) cc_final: 0.7496 (mp0) outliers start: 11 outliers final: 6 residues processed: 176 average time/residue: 0.3306 time to fit residues: 78.7769 Evaluate side-chains 149 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 49 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 81 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 = 0.3944 r_free = 0.3944 target = 0.142830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.086120 restraints weight = 35354.732| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.94 r_work: 0.2894 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14884 Z= 0.152 Angle : 0.558 7.570 21373 Z= 0.321 Chirality : 0.034 0.143 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.333 158.159 4324 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.63 % Allowed : 15.23 % Favored : 83.14 % 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: 1.47 (0.27), residues: 989 helix: 2.06 (0.21), residues: 658 sheet: -0.06 (1.21), residues: 23 loop : -1.45 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 61 HIS 0.006 0.001 HIS K 65 PHE 0.014 0.001 PHE K 53 TYR 0.025 0.001 TYR H 121 ARG 0.007 0.000 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00111 ( 2) link_TRANS : angle 0.23972 ( 6) hydrogen bonds : bond 0.03752 ( 828) hydrogen bonds : angle 2.95994 ( 2106) metal coordination : bond 0.01392 ( 8) metal coordination : angle 2.55954 ( 9) covalent geometry : bond 0.00334 (14874) covalent geometry : angle 0.55589 (21358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8126 (pm20) cc_final: 0.7723 (pm20) REVERT: B 84 MET cc_start: 0.8843 (mmm) cc_final: 0.8338 (mmm) REVERT: D 68 ASP cc_start: 0.9016 (t70) cc_final: 0.8709 (t0) REVERT: D 83 TYR cc_start: 0.8743 (m-10) cc_final: 0.8331 (m-80) REVERT: D 101 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8642 (mp) REVERT: F 25 ASN cc_start: 0.8485 (m110) cc_final: 0.7957 (m-40) REVERT: F 91 LYS cc_start: 0.8974 (ttmt) cc_final: 0.8740 (ttpp) REVERT: K 20 MET cc_start: 0.6967 (mmp) cc_final: 0.6617 (mpp) REVERT: L 30 MET cc_start: 0.6293 (mmm) cc_final: 0.5922 (ptt) REVERT: C 24 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8637 (mm-40) REVERT: C 61 GLU cc_start: 0.8550 (tp30) cc_final: 0.8253 (tt0) REVERT: C 92 GLU cc_start: 0.8414 (mp0) cc_final: 0.8077 (mp0) REVERT: C 104 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8660 (tp40) REVERT: G 36 LYS cc_start: 0.8306 (pttt) cc_final: 0.7766 (mmtp) REVERT: G 72 ASP cc_start: 0.8891 (m-30) cc_final: 0.8506 (m-30) outliers start: 14 outliers final: 5 residues processed: 157 average time/residue: 0.3381 time to fit residues: 71.4874 Evaluate side-chains 149 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.138861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081988 restraints weight = 29100.907| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.67 r_work: 0.2835 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14884 Z= 0.238 Angle : 0.601 8.086 21373 Z= 0.342 Chirality : 0.037 0.138 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.765 157.394 4324 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.74 % Allowed : 15.93 % Favored : 82.33 % 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: 1.30 (0.27), residues: 989 helix: 1.89 (0.21), residues: 657 sheet: 0.12 (1.11), residues: 23 loop : -1.40 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.016 0.002 PHE K 53 TYR 0.031 0.002 TYR H 121 ARG 0.004 0.000 ARG H 79 Details of bonding type rmsd link_TRANS : bond 0.00304 ( 2) link_TRANS : angle 0.29794 ( 6) hydrogen bonds : bond 0.04347 ( 828) hydrogen bonds : angle 3.20348 ( 2106) metal coordination : bond 0.01649 ( 8) metal coordination : angle 2.71318 ( 9) covalent geometry : bond 0.00552 (14874) covalent geometry : angle 0.59859 (21358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5797 (ptt-90) REVERT: D 68 ASP cc_start: 0.9099 (t70) cc_final: 0.8714 (t0) REVERT: F 25 ASN cc_start: 0.8502 (m110) cc_final: 0.7994 (m-40) REVERT: F 91 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8757 (ttpp) REVERT: K 64 TYR cc_start: 0.8757 (t80) cc_final: 0.8409 (t80) REVERT: C 61 GLU cc_start: 0.8594 (tp30) cc_final: 0.8208 (tt0) REVERT: C 92 GLU cc_start: 0.8402 (mp0) cc_final: 0.8146 (mp0) REVERT: C 104 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8633 (tp40) REVERT: G 36 LYS cc_start: 0.8237 (pttt) cc_final: 0.7794 (mmtp) REVERT: G 92 GLU cc_start: 0.8646 (mp0) cc_final: 0.7796 (mp0) outliers start: 15 outliers final: 7 residues processed: 147 average time/residue: 0.3416 time to fit residues: 66.9657 Evaluate side-chains 142 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 40 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.142826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.086215 restraints weight = 30898.355| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.77 r_work: 0.2907 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14884 Z= 0.146 Angle : 0.555 8.785 21373 Z= 0.320 Chirality : 0.034 0.150 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.227 159.081 4324 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.86 % Allowed : 16.40 % Favored : 81.74 % 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: 1.63 (0.27), residues: 989 helix: 2.12 (0.20), residues: 658 sheet: 0.28 (1.07), residues: 23 loop : -1.24 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 61 HIS 0.003 0.001 HIS A 113 PHE 0.017 0.001 PHE K 53 TYR 0.025 0.002 TYR H 121 ARG 0.004 0.000 ARG H 79 Details of bonding type rmsd link_TRANS : bond 0.00211 ( 2) link_TRANS : angle 0.43332 ( 6) hydrogen bonds : bond 0.03688 ( 828) hydrogen bonds : angle 2.89489 ( 2106) metal coordination : bond 0.01021 ( 8) metal coordination : angle 2.01242 ( 9) covalent geometry : bond 0.00319 (14874) covalent geometry : angle 0.55333 (21358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8747 (mmm) cc_final: 0.8250 (mmm) REVERT: D 68 ASP cc_start: 0.9009 (t70) cc_final: 0.8672 (t0) REVERT: F 25 ASN cc_start: 0.8492 (m110) cc_final: 0.7987 (m-40) REVERT: F 88 TYR cc_start: 0.8619 (m-80) cc_final: 0.8383 (m-80) REVERT: F 91 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8707 (ttpp) REVERT: H 37 TYR cc_start: 0.9097 (m-80) cc_final: 0.8852 (m-80) REVERT: K 20 MET cc_start: 0.7223 (mmm) cc_final: 0.6831 (mpp) REVERT: L 30 MET cc_start: 0.5945 (mmm) cc_final: 0.5014 (ptt) REVERT: C 23 LEU cc_start: 0.8707 (mt) cc_final: 0.8470 (mt) REVERT: C 61 GLU cc_start: 0.8558 (tp30) cc_final: 0.8252 (tt0) REVERT: C 92 GLU cc_start: 0.8346 (mp0) cc_final: 0.8093 (mp0) REVERT: C 104 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8683 (tp40) REVERT: G 36 LYS cc_start: 0.8199 (pttt) cc_final: 0.7711 (mmtp) REVERT: G 72 ASP cc_start: 0.8890 (m-30) cc_final: 0.8509 (m-30) REVERT: G 92 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8436 (mt-10) REVERT: G 104 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8609 (mm-40) outliers start: 16 outliers final: 11 residues processed: 146 average time/residue: 0.3467 time to fit residues: 67.2865 Evaluate side-chains 145 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 125 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.141620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.084021 restraints weight = 40810.702| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.09 r_work: 0.2859 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14884 Z= 0.173 Angle : 0.568 8.392 21373 Z= 0.326 Chirality : 0.035 0.142 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.393 158.418 4324 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.86 % Allowed : 16.63 % Favored : 81.51 % 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: 1.63 (0.27), residues: 989 helix: 2.12 (0.20), residues: 660 sheet: 0.34 (1.08), residues: 23 loop : -1.23 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.019 0.001 PHE K 53 TYR 0.025 0.002 TYR H 121 ARG 0.009 0.000 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00149 ( 2) link_TRANS : angle 0.22671 ( 6) hydrogen bonds : bond 0.03892 ( 828) hydrogen bonds : angle 2.97422 ( 2106) metal coordination : bond 0.01094 ( 8) metal coordination : angle 2.20872 ( 9) covalent geometry : bond 0.00393 (14874) covalent geometry : angle 0.56620 (21358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8771 (mmm) cc_final: 0.8215 (mmm) REVERT: D 68 ASP cc_start: 0.9072 (t70) cc_final: 0.8721 (t0) REVERT: F 25 ASN cc_start: 0.8424 (m110) cc_final: 0.7903 (m-40) REVERT: K 20 MET cc_start: 0.7285 (mmm) cc_final: 0.6936 (mpp) REVERT: L 30 MET cc_start: 0.6076 (mmm) cc_final: 0.5079 (ptt) REVERT: C 61 GLU cc_start: 0.8573 (tp30) cc_final: 0.8231 (tt0) REVERT: C 92 GLU cc_start: 0.8366 (mp0) cc_final: 0.8135 (mp0) REVERT: C 104 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8676 (tp40) REVERT: G 36 LYS cc_start: 0.8200 (pttt) cc_final: 0.7666 (mmtp) REVERT: G 104 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8578 (mm-40) outliers start: 16 outliers final: 11 residues processed: 154 average time/residue: 0.3359 time to fit residues: 69.6641 Evaluate side-chains 146 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 40 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.142691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.085133 restraints weight = 43827.707| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.21 r_work: 0.2871 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14884 Z= 0.151 Angle : 0.564 10.321 21373 Z= 0.323 Chirality : 0.034 0.142 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.265 158.627 4324 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.40 % Allowed : 17.56 % Favored : 81.05 % 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: 1.76 (0.27), residues: 989 helix: 2.20 (0.20), residues: 659 sheet: 0.38 (1.10), residues: 23 loop : -1.13 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 61 HIS 0.002 0.000 HIS K 65 PHE 0.019 0.001 PHE K 53 TYR 0.023 0.002 TYR H 121 ARG 0.007 0.000 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00089 ( 2) link_TRANS : angle 0.24137 ( 6) hydrogen bonds : bond 0.03707 ( 828) hydrogen bonds : angle 2.90053 ( 2106) metal coordination : bond 0.00918 ( 8) metal coordination : angle 1.89709 ( 9) covalent geometry : bond 0.00333 (14874) covalent geometry : angle 0.56255 (21358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8769 (mmm) cc_final: 0.8215 (mmm) REVERT: D 68 ASP cc_start: 0.9093 (t70) cc_final: 0.8749 (t0) REVERT: F 25 ASN cc_start: 0.8433 (m110) cc_final: 0.7916 (m-40) REVERT: F 88 TYR cc_start: 0.8634 (m-80) cc_final: 0.8321 (m-80) REVERT: H 37 TYR cc_start: 0.9114 (m-80) cc_final: 0.8876 (m-80) REVERT: K 20 MET cc_start: 0.7284 (mmm) cc_final: 0.6967 (mpp) REVERT: L 30 MET cc_start: 0.6155 (mmm) cc_final: 0.5254 (ptt) REVERT: C 61 GLU cc_start: 0.8576 (tp30) cc_final: 0.8257 (tt0) REVERT: C 92 GLU cc_start: 0.8370 (mp0) cc_final: 0.8138 (mp0) REVERT: C 104 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8672 (tp40) REVERT: G 36 LYS cc_start: 0.8182 (pttt) cc_final: 0.7678 (mmtp) REVERT: G 72 ASP cc_start: 0.8859 (m-30) cc_final: 0.8494 (m-30) REVERT: G 104 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8579 (mm-40) outliers start: 12 outliers final: 8 residues processed: 140 average time/residue: 0.3383 time to fit residues: 63.6054 Evaluate side-chains 140 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 40 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.142383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.084707 restraints weight = 46137.809| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.25 r_work: 0.2860 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14884 Z= 0.163 Angle : 0.574 10.081 21373 Z= 0.327 Chirality : 0.034 0.141 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.267 158.242 4324 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.28 % Allowed : 17.91 % Favored : 80.81 % 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: 1.75 (0.27), residues: 989 helix: 2.18 (0.20), residues: 660 sheet: 0.48 (1.13), residues: 23 loop : -1.13 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.021 0.001 PHE K 53 TYR 0.023 0.002 TYR H 121 ARG 0.006 0.000 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00121 ( 2) link_TRANS : angle 0.23460 ( 6) hydrogen bonds : bond 0.03775 ( 828) hydrogen bonds : angle 2.92315 ( 2106) metal coordination : bond 0.00746 ( 8) metal coordination : angle 1.86504 ( 9) covalent geometry : bond 0.00364 (14874) covalent geometry : angle 0.57258 (21358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8798 (mmm) cc_final: 0.8250 (mmm) REVERT: D 68 ASP cc_start: 0.9114 (t70) cc_final: 0.8774 (t0) REVERT: F 25 ASN cc_start: 0.8454 (m110) cc_final: 0.7933 (m-40) REVERT: H 37 TYR cc_start: 0.9141 (m-80) cc_final: 0.8902 (m-80) REVERT: K 20 MET cc_start: 0.7276 (mmm) cc_final: 0.6962 (mpp) REVERT: L 30 MET cc_start: 0.6005 (mmm) cc_final: 0.5165 (ptt) REVERT: C 61 GLU cc_start: 0.8602 (tp30) cc_final: 0.8280 (tt0) REVERT: C 92 GLU cc_start: 0.8411 (mp0) cc_final: 0.8181 (mp0) REVERT: C 104 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8707 (tp40) REVERT: G 36 LYS cc_start: 0.8215 (pttt) cc_final: 0.7708 (mmtp) REVERT: G 72 ASP cc_start: 0.8873 (m-30) cc_final: 0.8509 (m-30) REVERT: G 104 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8603 (mm-40) outliers start: 11 outliers final: 10 residues processed: 136 average time/residue: 0.3424 time to fit residues: 63.0164 Evaluate side-chains 141 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 40 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 99 optimal weight: 40.0000 chunk 91 optimal weight: 0.0970 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.142884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.086159 restraints weight = 32873.811| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.83 r_work: 0.2903 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14884 Z= 0.155 Angle : 0.571 9.972 21373 Z= 0.324 Chirality : 0.034 0.141 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.219 158.174 4324 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.28 % Allowed : 18.02 % Favored : 80.70 % 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: 1.84 (0.27), residues: 989 helix: 2.24 (0.20), residues: 659 sheet: 0.52 (1.13), residues: 23 loop : -1.07 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 61 HIS 0.003 0.000 HIS K 65 PHE 0.020 0.001 PHE K 53 TYR 0.022 0.002 TYR H 121 ARG 0.006 0.000 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00099 ( 2) link_TRANS : angle 0.24582 ( 6) hydrogen bonds : bond 0.03708 ( 828) hydrogen bonds : angle 2.89994 ( 2106) metal coordination : bond 0.00447 ( 8) metal coordination : angle 2.87058 ( 9) covalent geometry : bond 0.00347 (14874) covalent geometry : angle 0.56814 (21358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8779 (mmm) cc_final: 0.8246 (mmm) REVERT: D 68 ASP cc_start: 0.9105 (t70) cc_final: 0.8766 (t0) REVERT: D 101 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8593 (mp) REVERT: F 25 ASN cc_start: 0.8449 (m110) cc_final: 0.7928 (m-40) REVERT: H 37 TYR cc_start: 0.9114 (m-80) cc_final: 0.8876 (m-80) REVERT: L 30 MET cc_start: 0.6057 (mmm) cc_final: 0.5170 (ptt) REVERT: C 61 GLU cc_start: 0.8577 (tp30) cc_final: 0.8271 (tt0) REVERT: C 92 GLU cc_start: 0.8392 (mp0) cc_final: 0.8159 (mp0) REVERT: C 104 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8695 (tp40) REVERT: G 36 LYS cc_start: 0.8184 (pttt) cc_final: 0.7699 (mmtp) REVERT: G 72 ASP cc_start: 0.8879 (m-30) cc_final: 0.8516 (m-30) REVERT: G 89 ASN cc_start: 0.8623 (m-40) cc_final: 0.8405 (m-40) REVERT: G 104 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8571 (mm-40) outliers start: 11 outliers final: 9 residues processed: 140 average time/residue: 0.3315 time to fit residues: 62.7246 Evaluate side-chains 144 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 40 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.143418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.086206 restraints weight = 40783.967| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.10 r_work: 0.2893 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14884 Z= 0.149 Angle : 0.571 10.444 21373 Z= 0.324 Chirality : 0.034 0.140 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.165 158.053 4324 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.28 % Allowed : 18.02 % Favored : 80.70 % 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: 1.88 (0.27), residues: 989 helix: 2.27 (0.20), residues: 660 sheet: 0.66 (1.14), residues: 23 loop : -1.06 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 61 HIS 0.005 0.001 HIS K 65 PHE 0.023 0.001 PHE K 53 TYR 0.022 0.001 TYR H 121 ARG 0.006 0.000 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00080 ( 2) link_TRANS : angle 0.23154 ( 6) hydrogen bonds : bond 0.03669 ( 828) hydrogen bonds : angle 2.86683 ( 2106) metal coordination : bond 0.00333 ( 8) metal coordination : angle 1.81332 ( 9) covalent geometry : bond 0.00329 (14874) covalent geometry : angle 0.56982 (21358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8264.25 seconds wall clock time: 142 minutes 51.94 seconds (8571.94 seconds total)