Starting phenix.real_space_refine on Mon Jun 16 08:31:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8upf_42446/06_2025/8upf_42446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8upf_42446/06_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_42446/06_2025/8upf_42446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8upf_42446/06_2025/8upf_42446.map" model { file = "/net/cci-nas-00/data/ceres_data/8upf_42446/06_2025/8upf_42446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8upf_42446/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.02, per 1000 atoms: 0.64 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: 3.55 Conformation dependent library (CDL) restraints added in 1.4 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: 6.60 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: 5.01 Time building geometry restraints manager: 4.20 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 42.310 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.260 ------------------------------------------------------------------------------- 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 : 1.170 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: 0.4394 time to fit residues: 99.0722 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 : 1.025 ------------------------------------------------------------------------------- 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 = 0.138540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.081274 restraints weight = 34246.657| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.87 r_work: 0.2821 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- 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: 0.8085 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 4.81146 ( 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 : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8368 (pm20) cc_final: 0.8066 (pm20) REVERT: B 84 MET cc_start: 0.8957 (mmm) cc_final: 0.8343 (mmm) REVERT: D 68 ASP cc_start: 0.9117 (t70) cc_final: 0.8808 (t0) REVERT: D 108 LYS cc_start: 0.7613 (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: 0.8981 (ttmt) cc_final: 0.8756 (ttpp) REVERT: H 113 GLU cc_start: 0.8648 (tp30) cc_final: 0.7673 (tm-30) REVERT: K 20 MET cc_start: 0.7051 (mmp) cc_final: 0.6796 (mpp) REVERT: C 24 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8694 (mm-40) REVERT: C 61 GLU cc_start: 0.8628 (tp30) cc_final: 0.8117 (tt0) REVERT: C 92 GLU cc_start: 0.8353 (mp0) cc_final: 0.8047 (mp0) REVERT: C 104 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8852 (tp40) REVERT: G 36 LYS cc_start: 0.8240 (pttt) cc_final: 0.7705 (mmtp) REVERT: G 92 GLU cc_start: 0.8551 (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: 0.3681 time to fit residues: 75.9248 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 : 1.045 ------------------------------------------------------------------------------- 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: 0.9980 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.0170 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 K 81 GLN G 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.142712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.085528 restraints weight = 40471.891| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.12 r_work: 0.2879 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 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 = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14884 Z= 0.144 Angle : 0.552 6.843 21373 Z= 0.320 Chirality : 0.034 0.138 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.324 158.210 4324 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.40 % Allowed : 13.84 % Favored : 84.77 % 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: 0.97 (0.27), residues: 989 helix: 1.72 (0.20), residues: 657 sheet: -0.42 (1.16), residues: 23 loop : -1.71 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 61 HIS 0.005 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 0.00170 ( 2) link_TRANS : angle 0.38999 ( 6) hydrogen bonds : bond 0.03738 ( 828) hydrogen bonds : angle 2.98758 ( 2106) metal coordination : bond 0.01518 ( 8) metal coordination : angle 3.29709 ( 9) covalent geometry : bond 0.00309 (14874) covalent geometry : angle 0.54799 (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 170 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8168 (pm20) cc_final: 0.7801 (pm20) REVERT: B 84 MET cc_start: 0.8851 (mmm) cc_final: 0.8320 (mmm) REVERT: D 68 ASP cc_start: 0.9076 (t70) cc_final: 0.8779 (t0) REVERT: D 83 TYR cc_start: 0.8702 (m-10) cc_final: 0.8202 (m-80) REVERT: D 108 LYS cc_start: 0.7567 (ttpt) cc_final: 0.7367 (ttmm) REVERT: F 25 ASN cc_start: 0.8497 (m110) cc_final: 0.7962 (m-40) REVERT: F 77 LYS cc_start: 0.9147 (mttt) cc_final: 0.8941 (mtmt) REVERT: F 91 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8720 (ttpp) REVERT: H 113 GLU cc_start: 0.8575 (tp30) cc_final: 0.8180 (tm-30) REVERT: K 20 MET cc_start: 0.7181 (mmp) cc_final: 0.6822 (mpp) REVERT: L 30 MET cc_start: 0.6098 (mmm) cc_final: 0.5475 (ptt) REVERT: C 23 LEU cc_start: 0.8618 (mt) cc_final: 0.8389 (mt) REVERT: C 92 GLU cc_start: 0.8387 (mp0) cc_final: 0.8013 (mp0) REVERT: C 104 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8824 (tp40) REVERT: G 36 LYS cc_start: 0.8143 (pttt) cc_final: 0.7642 (mmtp) REVERT: G 92 GLU cc_start: 0.8572 (mp0) cc_final: 0.7674 (mp0) outliers start: 12 outliers final: 6 residues processed: 163 average time/residue: 0.3461 time to fit residues: 75.5782 Evaluate side-chains 147 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.142847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.086240 restraints weight = 35349.650| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.95 r_work: 0.2899 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 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 = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2427 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= 0.145 Angle : 0.549 6.895 21373 Z= 0.318 Chirality : 0.034 0.141 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.311 158.155 4324 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.86 % Allowed : 14.77 % Favored : 83.37 % 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: 1.42 (0.27), residues: 989 helix: 2.04 (0.21), residues: 658 sheet: -0.10 (1.19), residues: 23 loop : -1.49 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 77 HIS 0.005 0.001 HIS K 65 PHE 0.014 0.001 PHE K 53 TYR 0.025 0.001 TYR H 121 ARG 0.005 0.000 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00079 ( 2) link_TRANS : angle 0.24047 ( 6) hydrogen bonds : bond 0.03703 ( 828) hydrogen bonds : angle 2.92591 ( 2106) metal coordination : bond 0.01391 ( 8) metal coordination : angle 2.62273 ( 9) covalent geometry : bond 0.00316 (14874) covalent geometry : angle 0.54629 (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 165 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8133 (pm20) cc_final: 0.7731 (pm20) REVERT: B 84 MET cc_start: 0.8847 (mmm) cc_final: 0.8348 (mmm) REVERT: D 68 ASP cc_start: 0.9008 (t70) cc_final: 0.8716 (t0) REVERT: D 83 TYR cc_start: 0.8727 (m-10) cc_final: 0.8343 (m-80) REVERT: D 108 LYS cc_start: 0.7635 (ttpt) cc_final: 0.7406 (ttmm) REVERT: F 25 ASN cc_start: 0.8506 (m110) cc_final: 0.7967 (m-40) REVERT: F 91 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8727 (ttpp) REVERT: K 20 MET cc_start: 0.7011 (mmp) cc_final: 0.6686 (mpp) REVERT: C 23 LEU cc_start: 0.8694 (mt) cc_final: 0.8348 (mt) REVERT: C 24 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8630 (mm-40) REVERT: C 92 GLU cc_start: 0.8413 (mp0) cc_final: 0.8079 (mp0) REVERT: C 104 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8663 (tp40) REVERT: G 36 LYS cc_start: 0.8309 (pttt) cc_final: 0.7761 (mmtp) REVERT: G 72 ASP cc_start: 0.8900 (m-30) cc_final: 0.8516 (m-30) outliers start: 16 outliers final: 9 residues processed: 156 average time/residue: 0.3430 time to fit residues: 72.1753 Evaluate side-chains 152 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 36 SER 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 K residue 27 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER 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: 5.9990 chunk 60 optimal weight: 4.9990 chunk 92 optimal weight: 0.0770 chunk 105 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.139118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.082290 restraints weight = 29100.182| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.68 r_work: 0.2841 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 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 = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14884 Z= 0.227 Angle : 0.596 7.957 21373 Z= 0.339 Chirality : 0.037 0.142 2420 Planarity : 0.004 0.036 1691 Dihedral : 29.709 157.320 4324 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.51 % Allowed : 16.05 % Favored : 82.44 % 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: 1.32 (0.27), residues: 989 helix: 1.90 (0.21), residues: 657 sheet: 0.06 (1.11), residues: 23 loop : -1.38 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.016 0.002 PHE K 53 TYR 0.030 0.002 TYR H 121 ARG 0.004 0.000 ARG H 79 Details of bonding type rmsd link_TRANS : bond 0.00276 ( 2) link_TRANS : angle 0.31330 ( 6) hydrogen bonds : bond 0.04311 ( 828) hydrogen bonds : angle 3.17484 ( 2106) metal coordination : bond 0.01635 ( 8) metal coordination : angle 2.68133 ( 9) covalent geometry : bond 0.00527 (14874) covalent geometry : angle 0.59369 (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 146 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8067 (pm20) cc_final: 0.7796 (pm20) REVERT: D 68 ASP cc_start: 0.9095 (t70) cc_final: 0.8716 (t0) REVERT: D 108 LYS cc_start: 0.7689 (ttpt) cc_final: 0.7378 (mtpp) REVERT: F 25 ASN cc_start: 0.8501 (m110) cc_final: 0.7997 (m-40) REVERT: F 91 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8757 (ttpp) REVERT: K 64 TYR cc_start: 0.8742 (t80) cc_final: 0.8362 (t80) REVERT: L 30 MET cc_start: 0.6084 (mmm) cc_final: 0.5136 (ptt) REVERT: C 61 GLU cc_start: 0.8582 (tp30) cc_final: 0.8212 (tt0) REVERT: C 92 GLU cc_start: 0.8401 (mp0) cc_final: 0.8161 (mp0) REVERT: C 104 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8657 (tp40) REVERT: G 36 LYS cc_start: 0.8276 (pttt) cc_final: 0.7779 (mmtp) REVERT: G 92 GLU cc_start: 0.8644 (mp0) cc_final: 0.8441 (mt-10) outliers start: 13 outliers final: 7 residues processed: 137 average time/residue: 0.4058 time to fit residues: 74.4419 Evaluate side-chains 138 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 H residue 118 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.142110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.085865 restraints weight = 30912.577| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.72 r_work: 0.2901 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 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 = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2723 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 : 0.551 8.349 21373 Z= 0.319 Chirality : 0.034 0.147 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.312 158.445 4324 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.28 % Allowed : 16.63 % Favored : 82.09 % 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: 1.59 (0.27), residues: 989 helix: 2.09 (0.20), residues: 659 sheet: 0.27 (1.07), residues: 23 loop : -1.24 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.015 0.001 PHE K 53 TYR 0.026 0.002 TYR H 121 ARG 0.004 0.000 ARG H 79 Details of bonding type rmsd link_TRANS : bond 0.00143 ( 2) link_TRANS : angle 0.24553 ( 6) hydrogen bonds : bond 0.03735 ( 828) hydrogen bonds : angle 2.93890 ( 2106) metal coordination : bond 0.01138 ( 8) metal coordination : angle 2.25007 ( 9) covalent geometry : bond 0.00326 (14874) covalent geometry : angle 0.54948 (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 146 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8009 (pm20) cc_final: 0.7730 (pm20) REVERT: B 84 MET cc_start: 0.8757 (mmm) cc_final: 0.8259 (mmm) REVERT: D 68 ASP cc_start: 0.9062 (t70) cc_final: 0.8719 (t0) REVERT: D 108 LYS cc_start: 0.7607 (ttpt) cc_final: 0.7352 (ttmm) REVERT: F 25 ASN cc_start: 0.8482 (m110) cc_final: 0.7971 (m-40) REVERT: L 30 MET cc_start: 0.6051 (mmm) cc_final: 0.5152 (ptt) REVERT: C 61 GLU cc_start: 0.8558 (tp30) cc_final: 0.8245 (tt0) REVERT: C 92 GLU cc_start: 0.8343 (mp0) cc_final: 0.8090 (mp0) REVERT: C 104 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8664 (tp40) REVERT: G 36 LYS cc_start: 0.8247 (pttt) cc_final: 0.7728 (mmtp) REVERT: G 72 ASP cc_start: 0.8887 (m-30) cc_final: 0.8509 (m-30) REVERT: G 104 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8594 (mm-40) outliers start: 11 outliers final: 9 residues processed: 138 average time/residue: 0.3467 time to fit residues: 63.8347 Evaluate side-chains 141 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 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 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: 7.9990 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: 1.9990 chunk 120 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.140554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082773 restraints weight = 40892.485| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.10 r_work: 0.2830 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14884 Z= 0.193 Angle : 0.576 8.589 21373 Z= 0.329 Chirality : 0.035 0.142 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.513 157.922 4324 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.51 % Allowed : 16.86 % Favored : 81.63 % 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: 1.57 (0.27), residues: 989 helix: 2.04 (0.20), residues: 660 sheet: 0.20 (1.06), residues: 23 loop : -1.17 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 61 HIS 0.004 0.001 HIS K 65 PHE 0.016 0.001 PHE K 53 TYR 0.027 0.002 TYR H 121 ARG 0.011 0.000 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00195 ( 2) link_TRANS : angle 0.25963 ( 6) hydrogen bonds : bond 0.04036 ( 828) hydrogen bonds : angle 3.04668 ( 2106) metal coordination : bond 0.01273 ( 8) metal coordination : angle 2.41803 ( 9) covalent geometry : bond 0.00441 (14874) covalent geometry : angle 0.57401 (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 156 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8042 (pm20) cc_final: 0.7744 (pm20) REVERT: D 68 ASP cc_start: 0.9070 (t70) cc_final: 0.8696 (t0) REVERT: D 108 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7369 (mtpp) REVERT: F 25 ASN cc_start: 0.8457 (m110) cc_final: 0.7965 (m-40) REVERT: C 61 GLU cc_start: 0.8586 (tp30) cc_final: 0.8223 (tt0) REVERT: C 92 GLU cc_start: 0.8394 (mp0) cc_final: 0.8179 (mp0) REVERT: C 104 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8684 (tp40) REVERT: G 36 LYS cc_start: 0.8163 (pttt) cc_final: 0.7717 (mmtp) REVERT: G 104 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8615 (mm-40) outliers start: 13 outliers final: 7 residues processed: 149 average time/residue: 0.3461 time to fit residues: 69.8010 Evaluate side-chains 140 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.141815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.084352 restraints weight = 43863.580| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.18 r_work: 0.2856 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 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 = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14884 Z= 0.163 Angle : 0.568 8.927 21373 Z= 0.326 Chirality : 0.034 0.142 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.307 158.477 4324 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.05 % Allowed : 17.44 % 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: 1.68 (0.27), residues: 989 helix: 2.13 (0.20), residues: 658 sheet: 0.27 (1.09), residues: 23 loop : -1.12 (0.33), residues: 308 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 0.019 0.001 PHE K 53 TYR 0.024 0.002 TYR H 121 ARG 0.007 0.000 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00124 ( 2) link_TRANS : angle 0.24267 ( 6) hydrogen bonds : bond 0.03785 ( 828) hydrogen bonds : angle 2.93708 ( 2106) metal coordination : bond 0.01013 ( 8) metal coordination : angle 2.04774 ( 9) covalent geometry : bond 0.00364 (14874) covalent geometry : angle 0.56642 (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 141 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8053 (pm20) cc_final: 0.7754 (pm20) REVERT: B 84 MET cc_start: 0.8785 (mmm) cc_final: 0.8236 (mmm) REVERT: D 68 ASP cc_start: 0.9105 (t70) cc_final: 0.8755 (t0) REVERT: D 83 TYR cc_start: 0.8973 (m-10) cc_final: 0.8667 (m-80) REVERT: D 108 LYS cc_start: 0.7630 (ttpt) cc_final: 0.7386 (ttmm) REVERT: F 25 ASN cc_start: 0.8488 (m110) cc_final: 0.7993 (m-40) REVERT: L 30 MET cc_start: 0.5988 (mmm) cc_final: 0.4995 (ptt) REVERT: C 61 GLU cc_start: 0.8599 (tp30) cc_final: 0.8267 (tt0) REVERT: C 92 GLU cc_start: 0.8377 (mp0) cc_final: 0.8157 (mp0) REVERT: C 104 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8700 (tp40) REVERT: G 36 LYS cc_start: 0.8243 (pttt) cc_final: 0.7706 (mmtp) REVERT: G 104 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8622 (mm-40) outliers start: 9 outliers final: 8 residues processed: 136 average time/residue: 0.4328 time to fit residues: 80.6873 Evaluate side-chains 141 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 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: 9.9990 chunk 108 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.141889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.084204 restraints weight = 46101.541| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.28 r_work: 0.2853 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 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 = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2983 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= 0.162 Angle : 0.569 9.101 21373 Z= 0.326 Chirality : 0.034 0.142 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.294 158.283 4324 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.28 % Allowed : 17.79 % Favored : 80.93 % 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: 1.68 (0.27), residues: 989 helix: 2.12 (0.20), residues: 660 sheet: 0.42 (1.12), 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 0.020 0.001 PHE K 53 TYR 0.023 0.001 TYR H 121 ARG 0.006 0.000 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00126 ( 2) link_TRANS : angle 0.23494 ( 6) hydrogen bonds : bond 0.03788 ( 828) hydrogen bonds : angle 2.93256 ( 2106) metal coordination : bond 0.00753 ( 8) metal coordination : angle 2.01717 ( 9) covalent geometry : bond 0.00363 (14874) covalent geometry : angle 0.56728 (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 143 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8029 (pm20) cc_final: 0.7729 (pm20) REVERT: B 84 MET cc_start: 0.8796 (mmm) cc_final: 0.8239 (mmm) REVERT: D 68 ASP cc_start: 0.9107 (t70) cc_final: 0.8763 (t0) REVERT: D 101 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8583 (mp) REVERT: D 108 LYS cc_start: 0.7627 (ttpt) cc_final: 0.7424 (ttmm) REVERT: F 25 ASN cc_start: 0.8471 (m110) cc_final: 0.7998 (m-40) REVERT: H 37 TYR cc_start: 0.9135 (m-80) cc_final: 0.8891 (m-80) REVERT: K 68 ARG cc_start: 0.8151 (ptp-170) cc_final: 0.7900 (ptp-170) REVERT: L 30 MET cc_start: 0.6339 (mmm) cc_final: 0.5387 (ptt) REVERT: C 61 GLU cc_start: 0.8602 (tp30) cc_final: 0.8272 (tt0) REVERT: C 92 GLU cc_start: 0.8387 (mp0) cc_final: 0.8169 (mp0) REVERT: C 104 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8707 (tp40) REVERT: G 36 LYS cc_start: 0.8235 (pttt) cc_final: 0.7707 (mmtp) REVERT: G 104 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8588 (mm-40) outliers start: 11 outliers final: 9 residues processed: 138 average time/residue: 0.4180 time to fit residues: 78.0677 Evaluate side-chains 142 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 112 ILE Chi-restraints excluded: chain E residue 117 VAL 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 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: 0.9990 chunk 64 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 99 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.141244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.084479 restraints weight = 32873.128| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.81 r_work: 0.2877 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- 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: 0.8016 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14884 Z= 0.184 Angle : 0.578 9.369 21373 Z= 0.329 Chirality : 0.035 0.141 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.353 157.836 4324 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.93 % Allowed : 18.14 % Favored : 80.93 % 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: 1.70 (0.27), residues: 989 helix: 2.10 (0.20), residues: 660 sheet: 0.55 (1.14), residues: 23 loop : -1.04 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.020 0.001 PHE K 53 TYR 0.024 0.002 TYR H 121 ARG 0.006 0.000 ARG D 79 Details of bonding type rmsd link_TRANS : bond 0.00176 ( 2) link_TRANS : angle 0.24992 ( 6) hydrogen bonds : bond 0.03911 ( 828) hydrogen bonds : angle 2.99117 ( 2106) metal coordination : bond 0.00549 ( 8) metal coordination : angle 2.62747 ( 9) covalent geometry : bond 0.00421 (14874) covalent geometry : angle 0.57576 (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 143 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7997 (pm20) cc_final: 0.7693 (pm20) REVERT: B 84 MET cc_start: 0.8797 (mmm) cc_final: 0.8212 (mmm) REVERT: D 68 ASP cc_start: 0.9065 (t70) cc_final: 0.8704 (t0) REVERT: D 101 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8573 (mp) REVERT: D 108 LYS cc_start: 0.7606 (ttpt) cc_final: 0.7347 (mtpp) REVERT: F 25 ASN cc_start: 0.8443 (m110) cc_final: 0.7931 (m-40) REVERT: K 68 ARG cc_start: 0.8173 (ptp-170) cc_final: 0.7936 (ptp-170) REVERT: L 30 MET cc_start: 0.6365 (mmm) cc_final: 0.5397 (ptt) REVERT: C 61 GLU cc_start: 0.8554 (tp30) cc_final: 0.8205 (tt0) REVERT: C 92 GLU cc_start: 0.8370 (mp0) cc_final: 0.8162 (mp0) REVERT: C 104 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8654 (tp40) REVERT: G 36 LYS cc_start: 0.8224 (pttt) cc_final: 0.7647 (mmtp) outliers start: 8 outliers final: 7 residues processed: 140 average time/residue: 0.3542 time to fit residues: 66.9266 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 : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.143372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.086383 restraints weight = 40766.427| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.10 r_work: 0.2895 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 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 = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3155 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= 0.145 Angle : 0.561 10.347 21373 Z= 0.321 Chirality : 0.034 0.140 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.136 158.512 4324 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.16 % Allowed : 17.91 % Favored : 80.93 % 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: 2.25 (0.20), residues: 660 sheet: 0.77 (1.16), residues: 23 loop : -1.03 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 61 HIS 0.005 0.001 HIS K 65 PHE 0.021 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 0.00090 ( 2) link_TRANS : angle 0.21945 ( 6) hydrogen bonds : bond 0.03649 ( 828) hydrogen bonds : angle 2.85384 ( 2106) metal coordination : bond 0.00249 ( 8) metal coordination : angle 2.17865 ( 9) covalent geometry : bond 0.00316 (14874) covalent geometry : angle 0.55985 (21358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9314.00 seconds wall clock time: 164 minutes 54.14 seconds (9894.14 seconds total)