Starting phenix.real_space_refine on Sat Jul 4 13:16:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9z_64893/07_2026/9v9z_64893.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9z_64893/07_2026/9v9z_64893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9z_64893/07_2026/9v9z_64893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9z_64893/07_2026/9v9z_64893.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9z_64893/07_2026/9v9z_64893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9z_64893/07_2026/9v9z_64893.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 11107 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 1 6.06 5 P 263 5.49 5 S 18 5.16 5 C 6828 2.51 5 N 2280 2.21 5 O 2787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12177 Number of models: 1 Model: "" Number of chains: 13 Chain: "N" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 252 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "A" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2671 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2721 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39 SG CYS N 27 42.069 66.209 44.223 1.00 81.07 S ATOM 58 SG CYS N 30 41.155 66.871 40.663 1.00 80.06 S ATOM 146 SG CYS N 41 38.729 64.765 42.789 1.00 76.37 S ATOM 166 SG CYS N 44 41.877 63.286 41.707 1.00 80.28 S Time building chain proxies: 2.48, per 1000 atoms: 0.20 Number of scatterers: 12177 At special positions: 0 Unit cell: (126.5, 96.8, 118.8, 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 1 29.99 S 18 16.00 P 263 15.00 O 2787 8.00 N 2280 7.00 C 6828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 372.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 30 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 41 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 27 " Number of angles added : 6 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 12 sheets defined 65.1% alpha, 4.1% beta 127 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.575A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.604A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.752A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.729A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.897A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.675A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.504A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.746A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.618A pdb=" N SER D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.182A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.513A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.727A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.556A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.930A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.514A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.493A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 4.020A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 34 Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 55 through 59 removed outlier: 3.764A pdb=" N ASP O 58 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.038A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.658A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.136A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.918A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.163A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 4 through 7 removed outlier: 6.914A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU O 69 " --> pdb=" O PHE O 4 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS O 6 " --> pdb=" O LEU O 69 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU O 71 " --> pdb=" O LYS O 6 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL O 70 " --> pdb=" O ARG O 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG O 42 " --> pdb=" O VAL O 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'O' and resid 44 through 45 removed outlier: 3.573A pdb=" N PHE O 45 " --> pdb=" O LYS O 48 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 658 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2638 1.34 - 1.45: 3845 1.45 - 1.57: 5886 1.57 - 1.69: 524 1.69 - 1.81: 29 Bond restraints: 12922 Sorted by residual: bond pdb=" C3' DT J 57 " pdb=" C2' DT J 57 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DC I 53 " pdb=" C2' DC I 53 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG I 33 " pdb=" C2' DG I 33 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG I 44 " pdb=" C2' DG I 44 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 12917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 17131 1.21 - 2.43: 1240 2.43 - 3.64: 182 3.64 - 4.86: 16 4.86 - 6.07: 5 Bond angle restraints: 18574 Sorted by residual: angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 75 " pdb=" C4 DT I 75 " pdb=" O4 DT I 75 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT J 105 " pdb=" C4 DT J 105 " pdb=" O4 DT J 105 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I 127 " pdb=" C4 DT I 127 " pdb=" O4 DT I 127 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 18569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 5922 35.31 - 70.62: 1166 70.62 - 105.93: 16 105.93 - 141.24: 0 141.24 - 176.55: 2 Dihedral angle restraints: 7106 sinusoidal: 4625 harmonic: 2481 Sorted by residual: dihedral pdb=" CA GLU O 34 " pdb=" C GLU O 34 " pdb=" N GLY O 35 " pdb=" CA GLY O 35 " ideal model delta harmonic sigma weight residual -180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DT J 57 " pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " pdb=" P DT J 58 " ideal model delta sinusoidal sigma weight residual -140.00 36.55 -176.55 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 75.66 144.34 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 7103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1168 0.029 - 0.058: 642 0.058 - 0.087: 195 0.087 - 0.115: 111 0.115 - 0.144: 8 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-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 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE O 3 " pdb=" N ILE O 3 " pdb=" C ILE O 3 " pdb=" CB ILE O 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 2121 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 80 " -0.015 2.00e-02 2.50e+03 1.02e-02 2.09e+00 pdb=" CG TYR H 80 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR H 80 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR H 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 80 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR H 80 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 80 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR H 80 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO G 80 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 104 " -0.008 2.00e-02 2.50e+03 1.01e-02 1.79e+00 pdb=" CG PHE E 104 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE E 104 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE E 104 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 104 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 104 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 104 " -0.000 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 799 2.74 - 3.28: 10710 3.28 - 3.82: 22647 3.82 - 4.36: 26655 4.36 - 4.90: 39909 Nonbonded interactions: 100720 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.294 3.040 nonbonded pdb=" O ASP O 39 " pdb=" NH1 ARG O 72 " model vdw 2.310 3.120 nonbonded pdb=" OH TYR G 39 " pdb=" OE1 GLU H 68 " model vdw 2.321 3.040 nonbonded pdb=" NE2 GLN O 2 " pdb=" O LYS O 63 " model vdw 2.357 3.120 ... (remaining 100715 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 133) selection = (chain 'E' and resid 39 through 133) } ncs_group { reference = (chain 'B' and resid 22 through 100) selection = (chain 'F' and resid 22 through 100) } ncs_group { reference = (chain 'C' and resid 14 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 30 through 120) selection = chain 'H' } 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=1.00 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.570 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.005 0.039 12926 Z= 0.480 Angle : 0.671 6.452 18580 Z= 0.605 Chirality : 0.041 0.144 2124 Planarity : 0.003 0.037 1438 Dihedral : 26.087 176.551 5500 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.30), residues: 834 helix: 2.95 (0.23), residues: 537 sheet: -1.29 (1.18), residues: 19 loop : -0.34 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 76 TYR 0.024 0.001 TYR H 80 PHE 0.023 0.001 PHE E 104 TRP 0.003 0.001 TRP N 25 HIS 0.004 0.000 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.48 (12922) covalent geometry : angle 0.66766 / 0.61 (18574) hydrogen bonds : bond 0.11046 / 7.33 ( 725) hydrogen bonds : angle 3.62146 / 2.73 ( 1831) metal coordination : bond 0.00300 / 0.15 ( 4) metal coordination : angle 3.71515 / 2.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7221 (mt-10) REVERT: C 95 LYS cc_start: 0.8656 (tttt) cc_final: 0.8376 (tppt) REVERT: D 59 MET cc_start: 0.8372 (mmm) cc_final: 0.7882 (mmm) REVERT: E 59 GLU cc_start: 0.7817 (pm20) cc_final: 0.7478 (pm20) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.8121 time to fit residues: 118.8504 Evaluate side-chains 113 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN E 125 GLN G 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.161776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116893 restraints weight = 16076.119| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.25 r_work: 0.3178 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12926 Z= 0.153 Angle : 0.583 6.180 18580 Z= 0.354 Chirality : 0.043 0.229 2124 Planarity : 0.004 0.037 1438 Dihedral : 29.648 176.110 3805 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.19 % Allowed : 9.00 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.29), residues: 834 helix: 2.85 (0.22), residues: 547 sheet: -0.98 (1.19), residues: 19 loop : -0.57 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.011 0.001 TYR H 118 PHE 0.017 0.001 PHE E 104 TRP 0.009 0.003 TRP N 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (12922) covalent geometry : angle 0.58024 / 0.35 (18574) hydrogen bonds : bond 0.05597 / 3.66 ( 725) hydrogen bonds : angle 2.75990 / 2.03 ( 1831) metal coordination : bond 0.00275 / 0.14 ( 4) metal coordination : angle 3.16310 / 2.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7642 (mt-10) REVERT: C 95 LYS cc_start: 0.8822 (tttt) cc_final: 0.8485 (tppt) REVERT: D 30 ARG cc_start: 0.5511 (mtt180) cc_final: 0.5282 (mtt180) REVERT: D 68 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8313 (tp30) REVERT: D 102 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7078 (mm-30) REVERT: E 59 GLU cc_start: 0.8337 (pm20) cc_final: 0.8022 (pm20) REVERT: G 36 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7983 (mttt) REVERT: G 95 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.7981 (tmtm) REVERT: H 32 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5953 (pm20) outliers start: 23 outliers final: 8 residues processed: 123 average time/residue: 0.8423 time to fit residues: 109.3786 Evaluate side-chains 122 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 39 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN E 125 GLN H 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.156468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110569 restraints weight = 16119.176| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.15 r_work: 0.3063 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12926 Z= 0.187 Angle : 0.636 6.522 18580 Z= 0.370 Chirality : 0.046 0.219 2124 Planarity : 0.005 0.045 1438 Dihedral : 30.116 178.737 3805 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.88 % Allowed : 11.50 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.29), residues: 834 helix: 2.53 (0.22), residues: 548 sheet: -2.17 (1.69), residues: 9 loop : -0.96 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 129 TYR 0.018 0.002 TYR G 50 PHE 0.013 0.002 PHE D 62 TRP 0.005 0.001 TRP N 25 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (12922) covalent geometry : angle 0.63252 / 0.37 (18574) hydrogen bonds : bond 0.06979 / 4.66 ( 725) hydrogen bonds : angle 2.86330 / 2.10 ( 1831) metal coordination : bond 0.00352 / 0.18 ( 4) metal coordination : angle 3.86806 / 2.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.348 Fit side-chains REVERT: A 129 ARG cc_start: 0.8054 (tmt170) cc_final: 0.7756 (ttp80) REVERT: B 63 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7848 (mt-10) REVERT: D 30 ARG cc_start: 0.5578 (mtt180) cc_final: 0.5291 (mtt180) REVERT: D 68 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8390 (tp30) REVERT: D 102 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7284 (mm-30) REVERT: E 59 GLU cc_start: 0.8246 (pm20) cc_final: 0.7898 (pm20) REVERT: G 36 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7967 (mttt) REVERT: G 56 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: G 95 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8007 (tmtm) REVERT: H 32 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.6053 (pm20) outliers start: 28 outliers final: 11 residues processed: 126 average time/residue: 0.8780 time to fit residues: 116.7232 Evaluate side-chains 126 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 39 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.0020 chunk 99 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 40 optimal weight: 0.0050 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112764 restraints weight = 16035.043| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.16 r_work: 0.3089 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 12926 Z= 0.143 Angle : 0.595 6.038 18580 Z= 0.350 Chirality : 0.044 0.207 2124 Planarity : 0.004 0.040 1438 Dihedral : 30.118 177.125 3805 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.19 % Allowed : 13.43 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.29), residues: 834 helix: 2.78 (0.22), residues: 545 sheet: -2.12 (1.70), residues: 9 loop : -1.01 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.012 0.001 TYR H 118 PHE 0.008 0.001 PHE D 62 TRP 0.006 0.001 TRP N 25 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (12922) covalent geometry : angle 0.59291 / 0.35 (18574) hydrogen bonds : bond 0.05814 / 3.86 ( 725) hydrogen bonds : angle 2.80471 / 2.05 ( 1831) metal coordination : bond 0.00320 / 0.16 ( 4) metal coordination : angle 3.13256 / 2.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8136 (tmt170) cc_final: 0.7878 (ttp80) REVERT: B 63 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7820 (mt-10) REVERT: C 91 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: D 30 ARG cc_start: 0.5513 (mtt180) cc_final: 0.5259 (mtt180) REVERT: D 59 MET cc_start: 0.8821 (mmm) cc_final: 0.8395 (mmm) REVERT: D 102 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7199 (mm-30) REVERT: E 59 GLU cc_start: 0.8269 (pm20) cc_final: 0.8016 (pm20) REVERT: E 133 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6205 (mp0) REVERT: G 95 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.7985 (tmtm) REVERT: H 32 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6059 (pm20) REVERT: O 1 MET cc_start: 0.3694 (tpt) cc_final: 0.3417 (tpp) outliers start: 23 outliers final: 10 residues processed: 120 average time/residue: 0.8294 time to fit residues: 105.2114 Evaluate side-chains 123 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 39 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 71 optimal weight: 0.0870 chunk 79 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN ** O 41 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 = 0.3938 r_free = 0.3938 target = 0.156831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111363 restraints weight = 16166.130| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.16 r_work: 0.3065 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12926 Z= 0.163 Angle : 0.597 5.855 18580 Z= 0.350 Chirality : 0.044 0.216 2124 Planarity : 0.004 0.041 1438 Dihedral : 30.199 178.306 3805 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.46 % Allowed : 13.99 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.29), residues: 834 helix: 2.60 (0.22), residues: 548 sheet: -2.32 (1.64), residues: 9 loop : -1.08 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 71 TYR 0.012 0.002 TYR H 118 PHE 0.009 0.001 PHE B 61 TRP 0.008 0.002 TRP N 25 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (12922) covalent geometry : angle 0.59351 / 0.35 (18574) hydrogen bonds : bond 0.06194 / 4.13 ( 725) hydrogen bonds : angle 2.78324 / 2.04 ( 1831) metal coordination : bond 0.00343 / 0.17 ( 4) metal coordination : angle 3.46109 / 2.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 91 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: D 30 ARG cc_start: 0.5567 (mtt180) cc_final: 0.5311 (mtt180) REVERT: D 59 MET cc_start: 0.8793 (mmm) cc_final: 0.8297 (mmm) REVERT: D 68 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8484 (tp30) REVERT: D 102 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7172 (mm-30) REVERT: E 59 GLU cc_start: 0.8173 (pm20) cc_final: 0.7914 (pm20) REVERT: E 133 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6237 (mp0) REVERT: G 36 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7929 (mttt) REVERT: G 95 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.7971 (tmtm) REVERT: H 32 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.6063 (pm20) outliers start: 25 outliers final: 12 residues processed: 117 average time/residue: 0.8236 time to fit residues: 101.8357 Evaluate side-chains 124 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 39 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 0.0970 chunk 19 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 75 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN ** O 41 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 = 0.3939 r_free = 0.3939 target = 0.156813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111508 restraints weight = 15994.418| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.14 r_work: 0.3072 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12926 Z= 0.161 Angle : 0.605 5.686 18580 Z= 0.352 Chirality : 0.044 0.217 2124 Planarity : 0.004 0.052 1438 Dihedral : 30.254 178.619 3805 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.46 % Allowed : 14.54 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.29), residues: 834 helix: 2.56 (0.22), residues: 548 sheet: -2.61 (1.49), residues: 9 loop : -1.14 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 53 TYR 0.012 0.002 TYR H 118 PHE 0.009 0.001 PHE B 61 TRP 0.009 0.002 TRP N 25 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (12922) covalent geometry : angle 0.60205 / 0.35 (18574) hydrogen bonds : bond 0.06071 / 4.06 ( 725) hydrogen bonds : angle 2.75664 / 2.02 ( 1831) metal coordination : bond 0.00321 / 0.16 ( 4) metal coordination : angle 3.48467 / 2.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7290 (mp0) REVERT: B 29 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9084 (mm) REVERT: C 91 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: D 30 ARG cc_start: 0.5588 (mtt180) cc_final: 0.5330 (mtt180) REVERT: D 59 MET cc_start: 0.8782 (mmm) cc_final: 0.8290 (mmm) REVERT: D 60 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8305 (m-40) REVERT: D 68 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8467 (tp30) REVERT: D 73 GLU cc_start: 0.8717 (tp30) cc_final: 0.8493 (tp30) REVERT: D 90 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: D 102 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7155 (mm-30) REVERT: E 59 GLU cc_start: 0.8141 (pm20) cc_final: 0.7807 (pm20) REVERT: E 133 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: G 56 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: G 95 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7991 (tmtm) REVERT: H 32 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.6061 (pm20) outliers start: 25 outliers final: 12 residues processed: 117 average time/residue: 0.8138 time to fit residues: 100.5580 Evaluate side-chains 129 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN H 44 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109982 restraints weight = 16030.127| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.19 r_work: 0.3043 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12926 Z= 0.183 Angle : 0.617 6.328 18580 Z= 0.357 Chirality : 0.045 0.225 2124 Planarity : 0.005 0.042 1438 Dihedral : 30.283 179.223 3805 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.46 % Allowed : 14.82 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.29), residues: 834 helix: 2.49 (0.22), residues: 548 sheet: -2.79 (1.40), residues: 9 loop : -1.22 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 53 TYR 0.013 0.002 TYR H 118 PHE 0.011 0.002 PHE D 62 TRP 0.009 0.002 TRP N 25 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (12922) covalent geometry : angle 0.61315 / 0.36 (18574) hydrogen bonds : bond 0.06463 / 4.34 ( 725) hydrogen bonds : angle 2.79782 / 2.05 ( 1831) metal coordination : bond 0.00324 / 0.17 ( 4) metal coordination : angle 3.63106 / 2.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7291 (mp0) REVERT: B 29 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9048 (mm) REVERT: C 91 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: D 30 ARG cc_start: 0.5630 (mtt180) cc_final: 0.5364 (mtt180) REVERT: D 59 MET cc_start: 0.8805 (mmm) cc_final: 0.8363 (mmm) REVERT: D 68 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8455 (tp30) REVERT: D 102 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7264 (mm-30) REVERT: E 59 GLU cc_start: 0.8210 (pm20) cc_final: 0.7880 (pm20) REVERT: E 133 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: G 36 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7854 (mttt) REVERT: G 56 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: G 95 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8038 (tmtm) REVERT: H 32 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.6110 (pm20) outliers start: 25 outliers final: 13 residues processed: 119 average time/residue: 0.7784 time to fit residues: 97.7967 Evaluate side-chains 129 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 30.0000 chunk 66 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 30.0000 chunk 88 optimal weight: 50.0000 chunk 104 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN ** O 41 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 = 0.3937 r_free = 0.3937 target = 0.156568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107638 restraints weight = 15957.016| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.17 r_work: 0.3081 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12926 Z= 0.153 Angle : 0.605 6.442 18580 Z= 0.352 Chirality : 0.044 0.218 2124 Planarity : 0.004 0.041 1438 Dihedral : 30.278 179.132 3805 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.46 % Allowed : 16.07 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.29), residues: 834 helix: 2.57 (0.22), residues: 548 sheet: -2.78 (1.41), residues: 9 loop : -1.19 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 53 TYR 0.014 0.002 TYR F 88 PHE 0.008 0.001 PHE B 61 TRP 0.008 0.002 TRP N 25 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (12922) covalent geometry : angle 0.60170 / 0.35 (18574) hydrogen bonds : bond 0.06048 / 4.04 ( 725) hydrogen bonds : angle 2.77758 / 2.03 ( 1831) metal coordination : bond 0.00347 / 0.18 ( 4) metal coordination : angle 3.54598 / 2.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7335 (mp0) REVERT: B 29 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9084 (mm) REVERT: C 91 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: D 30 ARG cc_start: 0.5567 (mtt180) cc_final: 0.5299 (mtt180) REVERT: D 59 MET cc_start: 0.8816 (mmm) cc_final: 0.8321 (mmm) REVERT: D 68 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8391 (tp30) REVERT: D 102 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7174 (mm-30) REVERT: E 59 GLU cc_start: 0.8136 (pm20) cc_final: 0.7790 (pm20) REVERT: E 133 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: G 36 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7848 (mttt) REVERT: G 56 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: G 95 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7950 (tmtm) REVERT: H 32 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.6029 (pm20) outliers start: 25 outliers final: 13 residues processed: 117 average time/residue: 0.8090 time to fit residues: 100.1184 Evaluate side-chains 130 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN ** O 41 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 = 0.3934 r_free = 0.3934 target = 0.156444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107592 restraints weight = 16015.228| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.17 r_work: 0.3082 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12926 Z= 0.159 Angle : 0.593 5.462 18580 Z= 0.346 Chirality : 0.044 0.224 2124 Planarity : 0.004 0.042 1438 Dihedral : 30.284 179.107 3805 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.32 % Allowed : 15.65 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.29), residues: 834 helix: 2.55 (0.22), residues: 548 sheet: -2.80 (1.40), residues: 9 loop : -1.25 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.013 0.002 TYR H 118 PHE 0.008 0.001 PHE B 61 TRP 0.008 0.002 TRP N 25 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (12922) covalent geometry : angle 0.58964 / 0.35 (18574) hydrogen bonds : bond 0.06035 / 4.04 ( 725) hydrogen bonds : angle 2.74890 / 2.01 ( 1831) metal coordination : bond 0.00328 / 0.17 ( 4) metal coordination : angle 3.59486 / 2.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7456 (mp0) REVERT: C 71 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7710 (mtp85) REVERT: C 91 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: D 30 ARG cc_start: 0.5592 (mtt180) cc_final: 0.5320 (mtt180) REVERT: D 59 MET cc_start: 0.8827 (mmm) cc_final: 0.8341 (mmm) REVERT: D 60 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8357 (m-40) REVERT: D 68 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8390 (tp30) REVERT: D 90 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: D 102 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7202 (mm-30) REVERT: E 59 GLU cc_start: 0.8143 (pm20) cc_final: 0.7810 (pm20) REVERT: E 133 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: G 36 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7877 (mttt) REVERT: G 56 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: G 95 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.7987 (tmtm) REVERT: H 32 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.6063 (pm20) outliers start: 24 outliers final: 11 residues processed: 119 average time/residue: 0.9421 time to fit residues: 118.2688 Evaluate side-chains 128 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 39 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 40.0000 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 41 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 = 0.3935 r_free = 0.3935 target = 0.156470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110858 restraints weight = 16066.078| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.17 r_work: 0.3068 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 12926 Z= 0.207 Angle : 0.823 59.198 18580 Z= 0.499 Chirality : 0.045 0.225 2124 Planarity : 0.004 0.042 1438 Dihedral : 30.283 179.101 3805 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.63 % Allowed : 17.31 % Favored : 80.06 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.29), residues: 834 helix: 2.49 (0.22), residues: 548 sheet: -2.82 (1.39), residues: 9 loop : -1.26 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 53 TYR 0.013 0.002 TYR H 118 PHE 0.008 0.002 PHE B 61 TRP 0.008 0.002 TRP N 25 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 (12922) covalent geometry : angle 0.82060 / 0.50 (18574) hydrogen bonds : bond 0.06189 / 4.16 ( 725) hydrogen bonds : angle 2.75109 / 2.01 ( 1831) metal coordination : bond 0.00319 / 0.16 ( 4) metal coordination : angle 3.60467 / 2.54 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7311 (mtp85) REVERT: A 133 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7382 (mp0) REVERT: C 91 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: D 30 ARG cc_start: 0.5566 (mtt180) cc_final: 0.5291 (mtt180) REVERT: D 59 MET cc_start: 0.8787 (mmm) cc_final: 0.8268 (mmm) REVERT: D 68 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8453 (tp30) REVERT: D 90 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: D 102 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7233 (mm-30) REVERT: E 59 GLU cc_start: 0.8173 (pm20) cc_final: 0.7845 (pm20) REVERT: E 133 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: G 36 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7863 (mttt) REVERT: G 95 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8019 (tmtm) REVERT: H 32 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.6060 (pm20) outliers start: 19 outliers final: 11 residues processed: 116 average time/residue: 0.9521 time to fit residues: 116.5024 Evaluate side-chains 126 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 39 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 89 optimal weight: 40.0000 chunk 59 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 44 GLN ** O 41 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 = 0.3933 r_free = 0.3933 target = 0.156292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107494 restraints weight = 15945.823| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.18 r_work: 0.3076 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 12926 Z= 0.207 Angle : 0.823 59.198 18580 Z= 0.499 Chirality : 0.045 0.225 2124 Planarity : 0.004 0.042 1438 Dihedral : 30.283 179.101 3805 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.63 % Allowed : 17.17 % Favored : 80.19 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.29), residues: 834 helix: 2.49 (0.22), residues: 548 sheet: -2.82 (1.39), residues: 9 loop : -1.26 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 53 TYR 0.013 0.002 TYR H 118 PHE 0.008 0.002 PHE B 61 TRP 0.008 0.002 TRP N 25 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 (12922) covalent geometry : angle 0.82060 / 0.50 (18574) hydrogen bonds : bond 0.06189 / 4.16 ( 725) hydrogen bonds : angle 2.75109 / 2.01 ( 1831) metal coordination : bond 0.00319 / 0.16 ( 4) metal coordination : angle 3.60467 / 2.54 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4136.88 seconds wall clock time: 70 minutes 52.07 seconds (4252.07 seconds total)