Starting phenix.real_space_refine on Sat Sep 12 14:36:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lya_23590/09_2026/7lya_23590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lya_23590/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lya_23590/09_2026/7lya_23590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lya_23590/09_2026/7lya_23590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lya_23590/09_2026/7lya_23590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lya_23590/09_2026/7lya_23590.map" } 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-2.2.1-6174/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: 3.07, per 1000 atoms: 0.25 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: 0.79 Conformation dependent library (CDL) restraints added in 478.2 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: 1.73 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: 2.27 Time building geometry restraints manager: 1.12 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: 17315 1.59 - 3.17: 1304 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: 1.450 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:9.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- 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= 0.653 Angle : 0.829 7.927 18690 Z= 0.719 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 0.82853 / 0.72 (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 : 0.293 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: 0.8122 (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: 0.9499 time to fit residues: 107.5406 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 : 0.288 ------------------------------------------------------------------------------- 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: 10.0000 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.158865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117785 restraints weight = 19473.920| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.19 r_work: 0.3163 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1000 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= 0.147 Angle : 0.661 8.043 18690 Z= 0.385 Chirality : 0.048 0.290 2124 Planarity : 0.004 0.035 1349 Dihedral : 30.337 173.542 4059 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.81 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: 0.57 (0.29), residues: 752 helix: 1.26 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.01 (0.34), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 131 TYR 0.008 0.001 TYR G 50 PHE 0.011 0.001 PHE C 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.15 (12909) covalent geometry : angle 0.66075 / 0.39 (18684) hydrogen bonds : bond 0.06317 / 4.23 ( 749) hydrogen bonds : angle 2.90589 / 2.06 ( 1868) link_TRANS : bond 0.00065 / 0.03 ( 2) link_TRANS : angle 0.34678 / 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 97 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.239 Fit side-chains REVERT: D 35 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8210 (mt-10) REVERT: D 47 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: F 91 LYS cc_start: 0.8743 (tttt) cc_final: 0.8292 (ttpt) REVERT: C 99 ARG cc_start: 0.8224 (mmm160) cc_final: 0.8000 (mmm160) REVERT: G 92 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8170 (mt-10) outliers start: 8 outliers final: 1 residues processed: 91 average time/residue: 0.9553 time to fit residues: 91.3476 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 : 0.226 ------------------------------------------------------------------------------- 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: 2.9990 chunk 77 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.157240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116741 restraints weight = 14295.765| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.08 r_work: 0.3151 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12911 Z= 0.165 Angle : 0.632 6.614 18690 Z= 0.369 Chirality : 0.047 0.304 2124 Planarity : 0.004 0.037 1349 Dihedral : 30.420 173.176 4059 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.72 % Allowed : 9.84 % Favored : 88.44 % 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: 1.28 (0.30), residues: 752 helix: 1.76 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.70 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 99 TYR 0.009 0.001 TYR H 40 PHE 0.007 0.001 PHE B 61 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (12909) covalent geometry : angle 0.63193 / 0.37 (18684) hydrogen bonds : bond 0.06346 / 4.20 ( 749) hydrogen bonds : angle 2.80241 / 2.00 ( 1868) link_TRANS : bond 0.00057 / 0.03 ( 2) link_TRANS : angle 0.24770 / 0.13 ( 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 91 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.228 Fit side-chains REVERT: E 120 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8739 (mtt) REVERT: F 91 LYS cc_start: 0.8765 (tttt) cc_final: 0.8313 (ttpt) REVERT: C 99 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7934 (mmm160) REVERT: G 92 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8088 (mt-10) outliers start: 10 outliers final: 5 residues processed: 84 average time/residue: 0.8931 time to fit residues: 78.8669 Evaluate side-chains 89 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.4980 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.156028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115361 restraints weight = 13891.627| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.06 r_work: 0.3135 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 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: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12911 Z= 0.186 Angle : 0.655 6.476 18690 Z= 0.374 Chirality : 0.048 0.323 2124 Planarity : 0.004 0.038 1349 Dihedral : 30.583 175.667 4059 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.19 % Allowed : 10.78 % Favored : 87.03 % 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: 1.53 (0.30), residues: 752 helix: 1.90 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.44 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 42 TYR 0.009 0.002 TYR D 121 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 0.00390 / 0.19 (12909) covalent geometry : angle 0.65538 / 0.37 (18684) hydrogen bonds : bond 0.06717 / 4.46 ( 749) hydrogen bonds : angle 2.81565 / 2.02 ( 1868) link_TRANS : bond 0.00057 / 0.03 ( 2) link_TRANS : angle 0.22074 / 0.12 ( 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 97 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.252 Fit side-chains REVERT: E 120 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8775 (mtt) REVERT: C 92 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8117 (mt-10) REVERT: C 99 ARG cc_start: 0.8194 (mmm160) cc_final: 0.7947 (mmm160) REVERT: G 92 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8035 (mt-10) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.9042 time to fit residues: 83.8574 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 : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 79 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 8 optimal weight: 0.0170 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.157285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116561 restraints weight = 13994.531| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.07 r_work: 0.3151 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 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: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12911 Z= 0.136 Angle : 0.635 7.942 18690 Z= 0.367 Chirality : 0.047 0.305 2124 Planarity : 0.004 0.038 1349 Dihedral : 30.547 175.223 4059 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.19 % Allowed : 11.72 % Favored : 86.09 % 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: 2.06 (0.23), residues: 544 sheet: None (None), residues: 0 loop : -1.32 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 42 TYR 0.008 0.001 TYR B 51 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 0.00207 / 0.14 (12909) covalent geometry : angle 0.63541 / 0.37 (18684) hydrogen bonds : bond 0.06147 / 4.08 ( 749) hydrogen bonds : angle 2.80811 / 2.01 ( 1868) link_TRANS : bond 0.00043 / 0.02 ( 2) link_TRANS : angle 0.15118 / 0.07 ( 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 93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.268 Fit side-chains REVERT: E 120 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8717 (mtt) REVERT: C 99 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7936 (mmm160) REVERT: G 92 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8055 (mt-10) outliers start: 13 outliers final: 11 residues processed: 85 average time/residue: 0.9145 time to fit residues: 81.7837 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 : 0.298 ------------------------------------------------------------------------------- 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 F residue 79 LYS 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: 5.9990 chunk 8 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.157002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114963 restraints weight = 19230.421| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.27 r_work: 0.3117 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12911 Z= 0.162 Angle : 0.633 6.394 18690 Z= 0.364 Chirality : 0.047 0.314 2124 Planarity : 0.004 0.039 1349 Dihedral : 30.550 175.861 4059 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.88 % Allowed : 12.81 % Favored : 85.31 % 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: 1.81 (0.30), residues: 752 helix: 2.09 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.28 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 99 TYR 0.009 0.001 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 0.00321 / 0.16 (12909) covalent geometry : angle 0.63336 / 0.36 (18684) hydrogen bonds : bond 0.06300 / 4.18 ( 749) hydrogen bonds : angle 2.76747 / 1.98 ( 1868) link_TRANS : bond 0.00034 / 0.02 ( 2) link_TRANS : angle 0.17374 / 0.09 ( 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: 11 poor density : 82 time to evaluate : 0.306 Fit side-chains REVERT: E 120 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8782 (mtt) REVERT: C 92 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8177 (mt-10) REVERT: C 99 ARG cc_start: 0.8237 (mmm160) cc_final: 0.7981 (mmm160) REVERT: G 92 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8089 (mt-10) outliers start: 11 outliers final: 8 residues processed: 86 average time/residue: 0.8890 time to fit residues: 80.6339 Evaluate side-chains 91 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 63 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 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 = 0.3779 r_free = 0.3779 target = 0.155953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114631 restraints weight = 15636.541| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.13 r_work: 0.3120 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12911 Z= 0.186 Angle : 0.650 7.347 18690 Z= 0.371 Chirality : 0.048 0.318 2124 Planarity : 0.004 0.039 1349 Dihedral : 30.615 176.155 4059 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.50 % Allowed : 12.19 % Favored : 85.31 % 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 (0.30), residues: 752 helix: 2.04 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.27 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.010 0.002 TYR D 121 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 0.00393 / 0.19 (12909) covalent geometry : angle 0.64965 / 0.37 (18684) hydrogen bonds : bond 0.06680 / 4.43 ( 749) hydrogen bonds : angle 2.80751 / 2.01 ( 1868) link_TRANS : bond 0.00063 / 0.03 ( 2) link_TRANS : angle 0.20868 / 0.10 ( 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 95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.320 Fit side-chains REVERT: E 120 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8775 (mtt) REVERT: C 74 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8476 (mtpp) REVERT: C 92 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8166 (mt-10) REVERT: C 99 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7931 (mmm160) REVERT: G 92 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8073 (mt-10) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 0.9064 time to fit residues: 83.1075 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 : 0.227 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.156152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114183 restraints weight = 18151.492| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.23 r_work: 0.3106 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12911 Z= 0.168 Angle : 0.645 6.860 18690 Z= 0.369 Chirality : 0.047 0.314 2124 Planarity : 0.004 0.039 1349 Dihedral : 30.616 176.240 4059 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.34 % Allowed : 12.19 % 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: 1.78 (0.30), residues: 752 helix: 2.05 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.25 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.00334 / 0.17 (12909) covalent geometry : angle 0.64480 / 0.37 (18684) hydrogen bonds : bond 0.06584 / 4.37 ( 749) hydrogen bonds : angle 2.80458 / 2.01 ( 1868) link_TRANS : bond 0.00037 / 0.02 ( 2) link_TRANS : angle 0.18328 / 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 94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.314 Fit side-chains REVERT: E 120 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8788 (mtt) REVERT: C 25 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8591 (m-80) REVERT: C 74 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8481 (mtpp) REVERT: C 92 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8189 (mt-10) REVERT: C 99 ARG cc_start: 0.8226 (mmm160) cc_final: 0.7936 (mmm160) REVERT: G 92 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8091 (mt-10) outliers start: 14 outliers final: 10 residues processed: 85 average time/residue: 0.8648 time to fit residues: 77.5773 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 : 0.312 ------------------------------------------------------------------------------- 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 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 25 PHE 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: 1.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.156125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115231 restraints weight = 14236.479| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.08 r_work: 0.3133 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12911 Z= 0.175 Angle : 0.646 6.915 18690 Z= 0.369 Chirality : 0.047 0.315 2124 Planarity : 0.004 0.039 1349 Dihedral : 30.614 176.290 4059 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.19 % Allowed : 12.50 % Favored : 85.31 % 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: 1.78 (0.30), residues: 752 helix: 2.05 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.24 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 99 TYR 0.010 0.002 TYR D 121 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (12909) covalent geometry : angle 0.64574 / 0.37 (18684) hydrogen bonds : bond 0.06582 / 4.37 ( 749) hydrogen bonds : angle 2.79849 / 2.00 ( 1868) link_TRANS : bond 0.00048 / 0.02 ( 2) link_TRANS : angle 0.18873 / 0.10 ( 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 94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.263 Fit side-chains REVERT: E 120 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8766 (mtt) REVERT: C 25 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: C 74 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8460 (mtpp) REVERT: C 92 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8149 (mt-10) REVERT: C 99 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7909 (mmm160) REVERT: G 92 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8056 (mt-10) outliers start: 13 outliers final: 10 residues processed: 86 average time/residue: 0.8970 time to fit residues: 81.3166 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 : 0.311 ------------------------------------------------------------------------------- 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 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 25 PHE 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: 0.1980 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 82 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.2281 > 50:) chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.157135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116879 restraints weight = 14187.610| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.01 r_work: 0.3160 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12911 Z= 0.141 Angle : 0.631 6.956 18690 Z= 0.364 Chirality : 0.047 0.304 2124 Planarity : 0.004 0.038 1349 Dihedral : 30.584 176.056 4059 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.19 % Allowed : 12.50 % Favored : 85.31 % 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 (0.30), residues: 752 helix: 2.14 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.20 (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 0.007 0.001 PHE F 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (12909) covalent geometry : angle 0.63156 / 0.36 (18684) hydrogen bonds : bond 0.06150 / 4.09 ( 749) hydrogen bonds : angle 2.78899 / 2.00 ( 1868) link_TRANS : bond 0.00050 / 0.03 ( 2) link_TRANS : angle 0.14586 / 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 93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.307 Fit side-chains REVERT: E 120 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8700 (mtt) REVERT: C 25 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: C 74 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8445 (mtpp) REVERT: C 92 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8114 (mt-10) REVERT: C 99 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7883 (mmm160) REVERT: G 92 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8014 (mt-10) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.8863 time to fit residues: 79.4467 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 : 0.203 ------------------------------------------------------------------------------- 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 25 PHE 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: 0.6980 chunk 77 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.156645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115009 restraints weight = 19260.835| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.20 r_work: 0.3128 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 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 = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12911 Z= 0.174 Angle : 0.640 7.213 18690 Z= 0.366 Chirality : 0.047 0.317 2124 Planarity : 0.004 0.040 1349 Dihedral : 30.598 176.400 4059 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.34 % Allowed : 12.34 % Favored : 85.31 % 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: 1.84 (0.30), residues: 752 helix: 2.09 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.22 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 99 TYR 0.009 0.002 TYR D 121 PHE 0.012 0.002 PHE E 78 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (12909) covalent geometry : angle 0.64043 / 0.37 (18684) hydrogen bonds : bond 0.06437 / 4.28 ( 749) hydrogen bonds : angle 2.77695 / 1.99 ( 1868) link_TRANS : bond 0.00048 / 0.02 ( 2) link_TRANS : angle 0.20360 / 0.11 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3913.73 seconds wall clock time: 67 minutes 3.47 seconds (4023.47 seconds total)