Starting phenix.real_space_refine on Fri Jul 3 21:49:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lya_23590/07_2026/7lya_23590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lya_23590/07_2026/7lya_23590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lya_23590/07_2026/7lya_23590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lya_23590/07_2026/7lya_23590.map" model { file = "/net/cci-nas-00/data/ceres_data/7lya_23590/07_2026/7lya_23590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lya_23590/07_2026/7lya_23590.cif" } resolution = 2.91 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= 0.068 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: 5 Type Number sf(0) Gaussians P 293 5.49 5 S 14 5.16 5 C 6687 2.51 5 N 2275 2.21 5 O 2829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 12098 Number of models: 1 Model: "" Number of chains: 10 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: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} 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: 737 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: 735 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: "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: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 2.24, per 1000 atoms: 0.19 Number of scatterers: 12098 At special positions: 0 Unit cell: (86.604, 126.813, 117.534, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 293 15.00 O 2829 8.00 N 2275 7.00 C 6687 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: 0.93 Conformation dependent library (CDL) restraints added in 385.1 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.4% alpha, 3.1% beta 139 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.539A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.606A 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 132 removed outlier: 3.548A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.719A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.550A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.595A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.538A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.605A 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 132 removed outlier: 3.548A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.694A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.555A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.600A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.607A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.520A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.507A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.732A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.697A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.695A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.127A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.391A 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: 7.165A 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 96 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.378A 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 89 393 hydrogen bonds defined for protein. 1160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.28 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: 2063 1.33 - 1.45: 4276 1.45 - 1.57: 5962 1.57 - 1.68: 584 1.68 - 1.80: 24 Bond restraints: 12909 Sorted by residual: bond pdb=" C3' DA J 6 " pdb=" O3' DA J 6 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.20e+01 bond pdb=" C3' DG J 27 " pdb=" O3' DG J 27 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.11e+01 bond pdb=" C3' DC J -40 " pdb=" C2' DC J -40 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.79e+00 bond pdb=" N1 DC I 8 " pdb=" C6 DC I 8 " ideal model delta sigma weight residual 1.367 1.348 0.019 6.00e-03 2.78e+04 9.72e+00 ... (remaining 12904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 17337 1.59 - 3.17: 1282 3.17 - 4.76: 54 4.76 - 6.34: 8 6.34 - 7.93: 3 Bond angle restraints: 18684 Sorted by residual: angle pdb=" O4' DG J -49 " pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 106.00 102.88 3.12 6.00e-01 2.78e+00 2.70e+01 angle pdb=" O4' DG J 20 " pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT J -17 " pdb=" C4 DT J -17 " pdb=" O4 DT J -17 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" O4' DC J 52 " pdb=" C4' DC J 52 " pdb=" C3' DC J 52 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT I -42 " pdb=" C4 DT I -42 " pdb=" O4 DT I -42 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 18679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 5579 34.23 - 68.45: 1430 68.45 - 102.68: 16 102.68 - 136.91: 0 136.91 - 171.14: 2 Dihedral angle restraints: 7027 sinusoidal: 4802 harmonic: 2225 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 48.86 171.14 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 71.26 148.74 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta harmonic sigma weight residual -180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1181 0.037 - 0.073: 647 0.073 - 0.110: 242 0.110 - 0.147: 50 0.147 - 0.184: 4 Chirality restraints: 2124 Sorted by residual: chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" C3' DC I 7 " pdb=" C4' DC I 7 " pdb=" O3' DC I 7 " pdb=" C2' DC I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" C3' DC J -20 " pdb=" C4' DC J -20 " pdb=" O3' DC J -20 " pdb=" C2' DC J -20 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 2121 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -52 " -0.007 2.00e-02 2.50e+03 1.17e-02 4.10e+00 pdb=" N9 DG I -52 " -0.001 2.00e-02 2.50e+03 pdb=" C8 DG I -52 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -52 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -52 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG I -52 " 0.012 2.00e-02 2.50e+03 pdb=" O6 DG I -52 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DG I -52 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DG I -52 " 0.030 2.00e-02 2.50e+03 pdb=" N2 DG I -52 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DG I -52 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -52 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.026 2.00e-02 2.50e+03 1.09e-02 3.53e+00 pdb=" N9 DG I 47 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 57 " 0.024 2.00e-02 2.50e+03 1.05e-02 3.03e+00 pdb=" N9 DA I 57 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 57 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 57 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 57 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 57 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 57 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 57 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 57 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 57 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 57 " -0.004 2.00e-02 2.50e+03 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 724 2.72 - 3.26: 10122 3.26 - 3.81: 21513 3.81 - 4.35: 28626 4.35 - 4.90: 40516 Nonbonded interactions: 101501 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.173 2.496 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.253 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.253 3.120 nonbonded pdb=" N3 DC I 21 " pdb=" N1 DG J -21 " model vdw 2.301 2.560 ... (remaining 101496 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' 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' and resid 11 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 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=0.50 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.860 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 0.046 12911 Z= 0.652 Angle : 0.821 7.927 18690 Z= 0.712 Chirality : 0.049 0.184 2124 Planarity : 0.004 0.040 1349 Dihedral : 27.352 171.135 5589 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.16 % Allowed : 1.88 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.91 (0.26), residues: 752 helix: -0.60 (0.20), residues: 537 sheet: None (None), residues: 0 loop : -2.78 (0.30), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 20 TYR 0.012 0.002 TYR B 51 PHE 0.010 0.002 PHE E 84 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00838 / 0.65 (12909) covalent geometry : angle 0.82068 / 0.71 (18684) hydrogen bonds : bond 0.13015 / 8.55 ( 749) hydrogen bonds : angle 4.73667 / 3.33 ( 1868) link_TRANS : bond 0.00284 / 0.15 ( 2) link_TRANS : angle 1.06617 / 0.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.280 Fit side-chains REVERT: D 35 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8124 (mt-10) REVERT: D 47 GLN cc_start: 0.7886 (mt0) cc_final: 0.7393 (mt0) REVERT: E 133 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8159 (mt-10) REVERT: F 52 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8121 (tp30) REVERT: F 91 LYS cc_start: 0.8465 (tttt) cc_final: 0.7992 (ttpt) REVERT: C 92 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7823 (mt-10) REVERT: C 99 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7680 (mmm160) REVERT: G 92 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7774 (mt-10) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.9450 time to fit residues: 107.0895 Evaluate side-chains 85 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 47 GLN F 27 GLN F 75 HIS H 49 HIS C 24 GLN C 73 ASN G 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.158544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117403 restraints weight = 19468.807| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.20 r_work: 0.3162 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12911 Z= 0.150 Angle : 0.647 7.957 18690 Z= 0.381 Chirality : 0.047 0.274 2124 Planarity : 0.004 0.035 1349 Dihedral : 30.424 174.049 4059 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.41 % Allowed : 8.91 % Favored : 89.69 % 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: 0.48 (0.29), residues: 752 helix: 1.19 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.03 (0.34), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 42 TYR 0.009 0.001 TYR G 50 PHE 0.008 0.001 PHE C 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.15 (12909) covalent geometry : angle 0.64717 / 0.38 (18684) hydrogen bonds : bond 0.06390 / 4.27 ( 749) hydrogen bonds : angle 2.92596 / 2.08 ( 1868) link_TRANS : bond 0.00069 / 0.04 ( 2) link_TRANS : angle 0.35606 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.298 Fit side-chains REVERT: D 35 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8183 (mt-10) REVERT: D 47 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: F 91 LYS cc_start: 0.8718 (tttt) cc_final: 0.8244 (ttpt) REVERT: C 99 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7966 (mmm160) REVERT: G 92 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8141 (mt-10) outliers start: 8 outliers final: 1 residues processed: 91 average time/residue: 0.9335 time to fit residues: 89.4064 Evaluate side-chains 83 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain C residue 74 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 10.9990 chunk 97 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114782 restraints weight = 14288.872| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.08 r_work: 0.3124 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12911 Z= 0.193 Angle : 0.646 6.555 18690 Z= 0.378 Chirality : 0.048 0.293 2124 Planarity : 0.005 0.038 1349 Dihedral : 30.577 173.728 4059 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.72 % Allowed : 9.69 % Favored : 88.59 % 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: 1.10 (0.30), residues: 752 helix: 1.63 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.77 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 42 TYR 0.010 0.002 TYR D 121 PHE 0.008 0.002 PHE F 61 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (12909) covalent geometry : angle 0.64655 / 0.38 (18684) hydrogen bonds : bond 0.06911 / 4.58 ( 749) hydrogen bonds : angle 2.87976 / 2.06 ( 1868) link_TRANS : bond 0.00089 / 0.05 ( 2) link_TRANS : angle 0.28005 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.324 Fit side-chains REVERT: E 120 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8765 (mtt) REVERT: F 91 LYS cc_start: 0.8762 (tttt) cc_final: 0.8316 (ttpt) REVERT: C 99 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7960 (mmm160) REVERT: G 92 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8076 (mt-10) outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 1.0074 time to fit residues: 87.9025 Evaluate side-chains 85 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 74 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114901 restraints weight = 13886.373| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.07 r_work: 0.3130 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12911 Z= 0.193 Angle : 0.651 6.696 18690 Z= 0.378 Chirality : 0.048 0.298 2124 Planarity : 0.004 0.039 1349 Dihedral : 30.604 174.521 4059 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.03 % Allowed : 10.78 % Favored : 87.19 % 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: 1.29 (0.30), residues: 752 helix: 1.76 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 131 TYR 0.010 0.002 TYR D 121 PHE 0.008 0.002 PHE F 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (12909) covalent geometry : angle 0.65116 / 0.38 (18684) hydrogen bonds : bond 0.06843 / 4.54 ( 749) hydrogen bonds : angle 2.84990 / 2.04 ( 1868) link_TRANS : bond 0.00048 / 0.02 ( 2) link_TRANS : angle 0.25507 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.336 Fit side-chains REVERT: E 120 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8773 (mtt) REVERT: F 91 LYS cc_start: 0.8762 (tttt) cc_final: 0.8318 (ttpt) REVERT: C 99 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7959 (mmm160) REVERT: G 92 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8095 (mt-10) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.9689 time to fit residues: 84.6671 Evaluate side-chains 92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 74 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116598 restraints weight = 13993.972| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.01 r_work: 0.3159 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12911 Z= 0.147 Angle : 0.631 7.080 18690 Z= 0.369 Chirality : 0.047 0.283 2124 Planarity : 0.004 0.036 1349 Dihedral : 30.576 173.994 4059 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.03 % Allowed : 11.09 % Favored : 86.88 % 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: 1.51 (0.30), residues: 752 helix: 1.91 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.52 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 42 TYR 0.009 0.001 TYR D 121 PHE 0.008 0.001 PHE F 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.15 (12909) covalent geometry : angle 0.63104 / 0.37 (18684) hydrogen bonds : bond 0.06313 / 4.19 ( 749) hydrogen bonds : angle 2.83357 / 2.02 ( 1868) link_TRANS : bond 0.00026 / 0.01 ( 2) link_TRANS : angle 0.18056 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.344 Fit side-chains REVERT: E 120 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8706 (mtt) REVERT: F 91 LYS cc_start: 0.8745 (tttt) cc_final: 0.8298 (ttpt) REVERT: C 99 ARG cc_start: 0.8178 (mmm160) cc_final: 0.7930 (mmm160) REVERT: G 92 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8035 (mt-10) outliers start: 12 outliers final: 10 residues processed: 85 average time/residue: 0.9178 time to fit residues: 82.1431 Evaluate side-chains 92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 50 optimal weight: 0.0470 chunk 98 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115692 restraints weight = 19219.275| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.20 r_work: 0.3138 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12911 Z= 0.142 Angle : 0.625 7.271 18690 Z= 0.365 Chirality : 0.046 0.277 2124 Planarity : 0.004 0.036 1349 Dihedral : 30.565 174.564 4059 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.72 % Allowed : 11.56 % Favored : 86.72 % 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: 1.65 (0.30), residues: 752 helix: 2.01 (0.23), residues: 544 sheet: None (None), residues: 0 loop : -1.45 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 99 TYR 0.009 0.001 TYR D 121 PHE 0.007 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (12909) covalent geometry : angle 0.62531 / 0.37 (18684) hydrogen bonds : bond 0.06180 / 4.10 ( 749) hydrogen bonds : angle 2.79438 / 2.00 ( 1868) link_TRANS : bond 0.00041 / 0.02 ( 2) link_TRANS : angle 0.20143 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.260 Fit side-chains REVERT: E 120 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8751 (mtt) REVERT: F 91 LYS cc_start: 0.8744 (tttt) cc_final: 0.8273 (ttpt) REVERT: C 99 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7921 (mmm160) REVERT: G 92 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8083 (mt-10) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.8762 time to fit residues: 79.4918 Evaluate side-chains 90 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 16 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.0570 chunk 98 optimal weight: 0.8980 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112835 restraints weight = 15630.898| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.14 r_work: 0.3096 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12911 Z= 0.227 Angle : 0.675 6.463 18690 Z= 0.385 Chirality : 0.050 0.310 2124 Planarity : 0.005 0.039 1349 Dihedral : 30.734 175.116 4059 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.03 % Allowed : 12.19 % Favored : 85.78 % 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: 1.50 (0.30), residues: 752 helix: 1.86 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.41 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 99 TYR 0.011 0.002 TYR D 121 PHE 0.011 0.002 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.23 (12909) covalent geometry : angle 0.67460 / 0.39 (18684) hydrogen bonds : bond 0.07344 / 4.87 ( 749) hydrogen bonds : angle 2.88934 / 2.06 ( 1868) link_TRANS : bond 0.00101 / 0.05 ( 2) link_TRANS : angle 0.26656 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.303 Fit side-chains REVERT: D 71 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: E 120 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8741 (mtt) REVERT: C 92 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8157 (mt-10) REVERT: C 99 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7952 (mmm160) REVERT: G 92 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8093 (mt-10) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 0.9143 time to fit residues: 82.7489 Evaluate side-chains 90 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 16 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113723 restraints weight = 18119.585| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.15 r_work: 0.3108 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12911 Z= 0.174 Angle : 0.654 6.447 18690 Z= 0.376 Chirality : 0.048 0.295 2124 Planarity : 0.004 0.041 1349 Dihedral : 30.721 175.037 4059 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.19 % Allowed : 12.03 % Favored : 85.78 % 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: 1.62 (0.30), residues: 752 helix: 1.94 (0.23), residues: 545 sheet: None (None), residues: 0 loop : -1.35 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 99 TYR 0.010 0.002 TYR B 51 PHE 0.009 0.002 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (12909) covalent geometry : angle 0.65441 / 0.38 (18684) hydrogen bonds : bond 0.06893 / 4.58 ( 749) hydrogen bonds : angle 2.88099 / 2.06 ( 1868) link_TRANS : bond 0.00033 / 0.02 ( 2) link_TRANS : angle 0.17339 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.328 Fit side-chains REVERT: E 120 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8729 (mtt) REVERT: C 92 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8125 (mt-10) REVERT: C 99 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7912 (mmm160) REVERT: G 92 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8021 (mt-10) outliers start: 13 outliers final: 11 residues processed: 85 average time/residue: 0.8675 time to fit residues: 77.6307 Evaluate side-chains 92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 16 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115555 restraints weight = 14202.102| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.01 r_work: 0.3141 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12911 Z= 0.152 Angle : 0.647 7.845 18690 Z= 0.373 Chirality : 0.048 0.286 2124 Planarity : 0.004 0.039 1349 Dihedral : 30.700 175.235 4059 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.88 % Allowed : 12.66 % Favored : 85.47 % 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: 1.70 (0.30), residues: 752 helix: 2.00 (0.23), residues: 545 sheet: None (None), residues: 0 loop : -1.30 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.010 0.002 TYR D 121 PHE 0.008 0.002 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (12909) covalent geometry : angle 0.64690 / 0.37 (18684) hydrogen bonds : bond 0.06559 / 4.36 ( 749) hydrogen bonds : angle 2.85139 / 2.04 ( 1868) link_TRANS : bond 0.00006 / 0.00 ( 2) link_TRANS : angle 0.16474 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.425 Fit side-chains REVERT: E 120 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8702 (mtt) REVERT: C 92 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8079 (mt-10) REVERT: C 99 ARG cc_start: 0.8157 (mmm160) cc_final: 0.7894 (mmm160) REVERT: G 92 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8006 (mt-10) outliers start: 11 outliers final: 10 residues processed: 84 average time/residue: 0.9419 time to fit residues: 83.4212 Evaluate side-chains 91 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 82 optimal weight: 0.0570 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.156317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116021 restraints weight = 14169.038| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.02 r_work: 0.3151 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12911 Z= 0.139 Angle : 0.640 9.885 18690 Z= 0.369 Chirality : 0.047 0.278 2124 Planarity : 0.004 0.039 1349 Dihedral : 30.685 175.369 4059 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.88 % Allowed : 12.66 % Favored : 85.47 % 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: 1.77 (0.31), residues: 752 helix: 2.05 (0.23), residues: 545 sheet: None (None), residues: 0 loop : -1.28 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 99 TYR 0.010 0.001 TYR B 51 PHE 0.010 0.001 PHE C 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (12909) covalent geometry : angle 0.64028 / 0.37 (18684) hydrogen bonds : bond 0.06391 / 4.25 ( 749) hydrogen bonds : angle 2.83505 / 2.03 ( 1868) link_TRANS : bond 0.00036 / 0.02 ( 2) link_TRANS : angle 0.14866 / 0.07 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.297 Fit side-chains REVERT: E 120 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8696 (mtt) REVERT: C 92 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8065 (mt-10) REVERT: C 99 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7891 (mmm160) REVERT: G 92 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7981 (mt-10) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.9892 time to fit residues: 88.4113 Evaluate side-chains 91 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 43 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112425 restraints weight = 19237.950| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.28 r_work: 0.3082 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12911 Z= 0.214 Angle : 0.666 7.761 18690 Z= 0.380 Chirality : 0.049 0.309 2124 Planarity : 0.005 0.042 1349 Dihedral : 30.754 175.761 4059 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.88 % Allowed : 12.50 % Favored : 85.62 % 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: 1.59 (0.30), residues: 752 helix: 1.92 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.35 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 99 TYR 0.011 0.002 TYR D 121 PHE 0.010 0.002 PHE A 78 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (12909) covalent geometry : angle 0.66646 / 0.38 (18684) hydrogen bonds : bond 0.07135 / 4.73 ( 749) hydrogen bonds : angle 2.87616 / 2.06 ( 1868) link_TRANS : bond 0.00088 / 0.04 ( 2) link_TRANS : angle 0.25613 / 0.13 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3985.66 seconds wall clock time: 68 minutes 21.00 seconds (4101.00 seconds total)