Starting phenix.real_space_refine on Wed Aug 5 13:35:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xsf_67179/08_2026/9xsf_67179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xsf_67179/08_2026/9xsf_67179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xsf_67179/08_2026/9xsf_67179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xsf_67179/08_2026/9xsf_67179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xsf_67179/08_2026/9xsf_67179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xsf_67179/08_2026/9xsf_67179.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 230 5.49 5 S 14 5.16 5 C 5631 2.51 5 N 1889 2.21 5 O 2348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10112 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 632 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "D" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 689 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "E" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 729 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "H" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 698 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2353 Classifications: {'DNA': 114} Link IDs: {'rna3p': 113} Chain: "J" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2361 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.88, per 1000 atoms: 0.19 Number of scatterers: 10112 At special positions: 0 Unit cell: (103.296, 98.454, 116.208, 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 230 15.00 O 2348 8.00 N 1889 7.00 C 5631 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 NAG-SER " NAG B 601 " - " SER B 47 " " NAG F 601 " - " SER F 47 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 126.1 milliseconds 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1266 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 75.9% alpha, 2.3% beta 102 base pairs and 182 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.727A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.000A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.778A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.732A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.561A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.519A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.276A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.547A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.716A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.727A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.778A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.733A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.562A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.519A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.275A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.548A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.716A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.004A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.859A pdb=" N TYR B 98 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.922A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.223A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.003A 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 removed outlier: 3.503A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.714A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 373 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 259 hydrogen bonds 498 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 182 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2359 1.34 - 1.45: 3060 1.45 - 1.57: 4850 1.57 - 1.69: 458 1.69 - 1.81: 24 Bond restraints: 10751 Sorted by residual: bond pdb=" C1' DT I 15 " pdb=" N1 DT I 15 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" C1' DT J -17 " pdb=" N1 DT J -17 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.32e+01 bond pdb=" C1' DC J -18 " pdb=" N1 DC J -18 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.29e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C1' DC J 56 " pdb=" N1 DC J 56 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 ... (remaining 10746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 13893 1.13 - 2.26: 1143 2.26 - 3.39: 417 3.39 - 4.53: 36 4.53 - 5.66: 9 Bond angle restraints: 15498 Sorted by residual: angle pdb=" O4' DG I -35 " pdb=" C4' DG I -35 " pdb=" C3' DG I -35 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.33e+01 angle pdb=" O4' DG J -49 " pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.12e+01 angle pdb=" N3 DT I 15 " pdb=" C4 DT I 15 " pdb=" O4 DT I 15 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" O4' DA I 17 " pdb=" C4' DA I 17 " pdb=" C3' DA I 17 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J 1 " pdb=" C4 DT J 1 " pdb=" O4 DT J 1 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 15493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 4803 34.03 - 68.05: 1045 68.05 - 102.07: 26 102.07 - 136.10: 1 136.10 - 170.12: 2 Dihedral angle restraints: 5877 sinusoidal: 3912 harmonic: 1965 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 49.88 170.12 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 77.91 142.09 1 3.50e+01 8.16e-04 1.40e+01 dihedral pdb=" C4' DT I 15 " pdb=" C3' DT I 15 " pdb=" O3' DT I 15 " pdb=" P DA I 16 " ideal model delta sinusoidal sigma weight residual 220.00 98.93 121.07 1 3.50e+01 8.16e-04 1.19e+01 ... (remaining 5874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1215 0.036 - 0.072: 266 0.072 - 0.108: 76 0.108 - 0.144: 142 0.144 - 0.180: 77 Chirality restraints: 1776 Sorted by residual: chirality pdb=" C3' DC J 7 " pdb=" C4' DC J 7 " pdb=" O3' DC J 7 " pdb=" C2' DC J 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" C3' DC I -25 " pdb=" C4' DC I -25 " pdb=" O3' DC I -25 " pdb=" C2' DC I -25 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" C3' DT I -24 " pdb=" C4' DT I -24 " pdb=" O3' DT I -24 " pdb=" C2' DT I -24 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.23e-01 ... (remaining 1773 not shown) Planarity restraints: 1161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J -50 " 0.010 2.00e-02 2.50e+03 1.92e-02 8.31e+00 pdb=" N1 DC J -50 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DC J -50 " -0.046 2.00e-02 2.50e+03 pdb=" O2 DC J -50 " 0.028 2.00e-02 2.50e+03 pdb=" N3 DC J -50 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC J -50 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC J -50 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DC J -50 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC J -50 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 51 " -0.001 2.00e-02 2.50e+03 1.27e-02 4.82e+00 pdb=" N9 DG I 51 " -0.006 2.00e-02 2.50e+03 pdb=" C8 DG I 51 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DG I 51 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 51 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 51 " 0.009 2.00e-02 2.50e+03 pdb=" O6 DG I 51 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 51 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 51 " 0.035 2.00e-02 2.50e+03 pdb=" N2 DG I 51 " -0.021 2.00e-02 2.50e+03 pdb=" N3 DG I 51 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 51 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 44 " -0.003 2.00e-02 2.50e+03 1.38e-02 4.26e+00 pdb=" N1 DC J 44 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DC J 44 " -0.031 2.00e-02 2.50e+03 pdb=" O2 DC J 44 " 0.014 2.00e-02 2.50e+03 pdb=" N3 DC J 44 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DC J 44 " -0.015 2.00e-02 2.50e+03 pdb=" N4 DC J 44 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DC J 44 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC J 44 " 0.006 2.00e-02 2.50e+03 ... (remaining 1158 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 72 2.57 - 3.15: 8194 3.15 - 3.73: 18639 3.73 - 4.32: 24419 4.32 - 4.90: 36071 Nonbonded interactions: 87395 Sorted by model distance: nonbonded pdb=" N2 DG I -51 " pdb=" O2 DC J 51 " model vdw 1.984 2.496 nonbonded pdb=" O LYS H 116 " pdb=" OG1 THR H 119 " model vdw 2.075 3.040 nonbonded pdb=" O LYS D 116 " pdb=" OG1 THR D 119 " model vdw 2.075 3.040 nonbonded pdb=" O SER D 112 " pdb=" OG1 THR D 115 " model vdw 2.123 3.040 nonbonded pdb=" O SER H 112 " pdb=" OG1 THR H 115 " model vdw 2.123 3.040 ... (remaining 87390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 59 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 601)) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 108) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 124) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 : 0.006 0.065 10753 Z= 0.493 Angle : 0.760 8.789 15502 Z= 0.643 Chirality : 0.058 0.180 1776 Planarity : 0.005 0.044 1161 Dihedral : 27.100 170.124 4611 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.74 (0.32), residues: 665 helix: 1.22 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.69 (0.38), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 20 TYR 0.017 0.002 TYR B 88 PHE 0.016 0.002 PHE G 25 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.49 (10751) covalent geometry : angle 0.75666 / 0.64 (15498) hydrogen bonds : bond 0.12905 / 8.60 ( 632) hydrogen bonds : angle 5.55376 / 3.82 ( 1605) link_NAG-SER : bond 0.02044 / 1.05 ( 2) link_NAG-SER : angle 4.65909 / 2.33 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.253 Fit side-chains REVERT: D 108 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7422 (ptpt) REVERT: D 120 LYS cc_start: 0.8222 (mttm) cc_final: 0.7976 (mttt) REVERT: E 83 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7666 (mtp-110) REVERT: E 134 ARG cc_start: 0.6783 (ptm-80) cc_final: 0.6166 (tpp80) REVERT: F 27 GLN cc_start: 0.8459 (mp10) cc_final: 0.7839 (tm-30) REVERT: H 49 HIS cc_start: 0.7919 (m90) cc_final: 0.7686 (m170) REVERT: H 120 LYS cc_start: 0.8631 (mttm) cc_final: 0.8275 (mtpt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1243 time to fit residues: 25.0913 Evaluate side-chains 114 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0010 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0470 chunk 74 optimal weight: 50.0000 overall best weight: 0.8686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 25 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 82 HIS H 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.154781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.112533 restraints weight = 22185.581| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.27 r_work: 0.3421 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10753 Z= 0.164 Angle : 0.636 8.457 15502 Z= 0.379 Chirality : 0.043 0.317 1776 Planarity : 0.005 0.039 1161 Dihedral : 30.596 178.873 3294 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.66 % Allowed : 9.06 % Favored : 88.28 % 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 (0.33), residues: 665 helix: 1.76 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.67 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.010 0.001 TYR G 50 PHE 0.007 0.001 PHE E 84 HIS 0.006 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.16 (10751) covalent geometry : angle 0.63243 / 0.38 (15498) hydrogen bonds : bond 0.07861 / 5.12 ( 632) hydrogen bonds : angle 3.59916 / 2.48 ( 1605) link_NAG-SER : bond 0.00913 / 0.48 ( 2) link_NAG-SER : angle 4.31666 / 2.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.181 Fit side-chains REVERT: D 108 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7404 (ptpt) REVERT: D 120 LYS cc_start: 0.8137 (mttm) cc_final: 0.7804 (mttt) REVERT: E 83 ARG cc_start: 0.8417 (mtp85) cc_final: 0.8075 (mtp-110) REVERT: E 134 ARG cc_start: 0.6904 (ptm-80) cc_final: 0.6506 (tpp80) REVERT: F 27 GLN cc_start: 0.8599 (mp10) cc_final: 0.8044 (tm-30) REVERT: H 120 LYS cc_start: 0.8618 (mttm) cc_final: 0.8167 (mtpt) outliers start: 15 outliers final: 11 residues processed: 132 average time/residue: 0.1022 time to fit residues: 18.1611 Evaluate side-chains 121 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 20 optimal weight: 0.2980 chunk 45 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 25 ASN B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS F 25 ASN G 24 GLN G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.152811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.109414 restraints weight = 22170.343| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.26 r_work: 0.3354 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10753 Z= 0.161 Angle : 0.615 8.923 15502 Z= 0.363 Chirality : 0.043 0.337 1776 Planarity : 0.004 0.033 1161 Dihedral : 30.781 179.475 3294 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.66 % Allowed : 11.90 % Favored : 85.44 % 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: 1.82 (0.33), residues: 665 helix: 1.96 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.47 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 79 TYR 0.026 0.002 TYR C 57 PHE 0.033 0.002 PHE E 84 HIS 0.006 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (10751) covalent geometry : angle 0.61116 / 0.36 (15498) hydrogen bonds : bond 0.07077 / 4.68 ( 632) hydrogen bonds : angle 3.18914 / 2.22 ( 1605) link_NAG-SER : bond 0.00735 / 0.38 ( 2) link_NAG-SER : angle 4.48270 / 2.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.196 Fit side-chains REVERT: C 64 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7987 (tm-30) REVERT: D 46 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8265 (ttmt) REVERT: D 108 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7422 (ptpt) REVERT: D 120 LYS cc_start: 0.8046 (mttm) cc_final: 0.7746 (mttt) REVERT: E 83 ARG cc_start: 0.8513 (mtp85) cc_final: 0.8090 (mtp-110) REVERT: E 97 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: E 134 ARG cc_start: 0.7029 (ptm-80) cc_final: 0.6393 (tpp80) REVERT: F 27 GLN cc_start: 0.8608 (mp10) cc_final: 0.8101 (tm-30) REVERT: H 46 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7625 (mmtt) REVERT: H 120 LYS cc_start: 0.8621 (mttm) cc_final: 0.8169 (mtpt) outliers start: 15 outliers final: 8 residues processed: 134 average time/residue: 0.1055 time to fit residues: 19.0151 Evaluate side-chains 123 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 50.0000 chunk 60 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.152171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.107778 restraints weight = 21458.947| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.41 r_work: 0.3338 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10753 Z= 0.136 Angle : 0.584 8.926 15502 Z= 0.347 Chirality : 0.041 0.339 1776 Planarity : 0.004 0.036 1161 Dihedral : 30.795 178.270 3294 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.84 % Allowed : 12.97 % Favored : 84.19 % 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: 2.11 (0.33), residues: 665 helix: 2.17 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.35 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.032 0.002 TYR D 83 PHE 0.011 0.001 PHE D 70 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (10751) covalent geometry : angle 0.58058 / 0.35 (15498) hydrogen bonds : bond 0.06825 / 4.52 ( 632) hydrogen bonds : angle 3.01501 / 2.12 ( 1605) link_NAG-SER : bond 0.00615 / 0.32 ( 2) link_NAG-SER : angle 4.08823 / 1.98 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.242 Fit side-chains REVERT: D 46 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8202 (ttmt) REVERT: D 86 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7811 (ttm-80) REVERT: D 120 LYS cc_start: 0.8055 (mttm) cc_final: 0.7754 (mttt) REVERT: E 83 ARG cc_start: 0.8483 (mtp85) cc_final: 0.8053 (mtp-110) REVERT: E 134 ARG cc_start: 0.7003 (ptm-80) cc_final: 0.6369 (tpp80) REVERT: F 27 GLN cc_start: 0.8596 (mp10) cc_final: 0.8065 (tm-30) REVERT: H 120 LYS cc_start: 0.8657 (mttm) cc_final: 0.8216 (tttp) outliers start: 16 outliers final: 7 residues processed: 135 average time/residue: 0.0974 time to fit residues: 17.4591 Evaluate side-chains 124 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 56 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 50.0000 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 67 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 84 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.151087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.104935 restraints weight = 21146.216| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.37 r_work: 0.3299 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10753 Z= 0.142 Angle : 0.585 9.254 15502 Z= 0.344 Chirality : 0.041 0.344 1776 Planarity : 0.004 0.035 1161 Dihedral : 30.849 178.364 3294 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.37 % Allowed : 14.39 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.33), residues: 665 helix: 2.14 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.32 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.040 0.002 TYR D 83 PHE 0.010 0.001 PHE D 70 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (10751) covalent geometry : angle 0.58178 / 0.34 (15498) hydrogen bonds : bond 0.06681 / 4.44 ( 632) hydrogen bonds : angle 2.93480 / 2.06 ( 1605) link_NAG-SER : bond 0.00628 / 0.32 ( 2) link_NAG-SER : angle 3.93421 / 1.93 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.209 Fit side-chains REVERT: C 95 LYS cc_start: 0.7648 (tptt) cc_final: 0.7196 (ttmm) REVERT: D 46 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8134 (ttmt) REVERT: D 62 MET cc_start: 0.8837 (mmm) cc_final: 0.8486 (mmm) REVERT: E 83 ARG cc_start: 0.8519 (mtp85) cc_final: 0.8099 (mtp-110) REVERT: E 134 ARG cc_start: 0.6992 (ptm-80) cc_final: 0.6386 (tpp80) REVERT: F 27 GLN cc_start: 0.8622 (mp10) cc_final: 0.8059 (tm-30) REVERT: H 120 LYS cc_start: 0.8626 (mttm) cc_final: 0.8202 (tttp) outliers start: 19 outliers final: 11 residues processed: 142 average time/residue: 0.1247 time to fit residues: 23.2923 Evaluate side-chains 132 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 70 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.151288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.105262 restraints weight = 21556.437| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.28 r_work: 0.3301 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10753 Z= 0.133 Angle : 0.581 9.174 15502 Z= 0.341 Chirality : 0.040 0.344 1776 Planarity : 0.004 0.034 1161 Dihedral : 30.840 177.909 3294 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.37 % Allowed : 15.81 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.33), residues: 665 helix: 2.19 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 79 TYR 0.049 0.002 TYR D 83 PHE 0.011 0.001 PHE D 70 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (10751) covalent geometry : angle 0.57796 / 0.34 (15498) hydrogen bonds : bond 0.06579 / 4.36 ( 632) hydrogen bonds : angle 2.89678 / 2.04 ( 1605) link_NAG-SER : bond 0.00589 / 0.30 ( 2) link_NAG-SER : angle 3.64260 / 1.78 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.267 Fit side-chains REVERT: C 95 LYS cc_start: 0.7642 (tptt) cc_final: 0.7149 (ttmm) REVERT: D 46 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8132 (ttmt) REVERT: D 62 MET cc_start: 0.8848 (mmm) cc_final: 0.8450 (mmm) REVERT: E 83 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8118 (mtt-85) REVERT: E 134 ARG cc_start: 0.7000 (ptm-80) cc_final: 0.6430 (tpp80) REVERT: F 27 GLN cc_start: 0.8647 (mp10) cc_final: 0.8073 (tm-30) REVERT: H 120 LYS cc_start: 0.8607 (mttm) cc_final: 0.8283 (tttp) outliers start: 19 outliers final: 14 residues processed: 137 average time/residue: 0.0995 time to fit residues: 18.4578 Evaluate side-chains 136 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 74 optimal weight: 40.0000 chunk 33 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 84 optimal weight: 50.0000 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 38 ASN G 84 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.149791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103107 restraints weight = 21174.411| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.25 r_work: 0.3257 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10753 Z= 0.158 Angle : 0.610 9.476 15502 Z= 0.351 Chirality : 0.041 0.348 1776 Planarity : 0.004 0.035 1161 Dihedral : 30.886 178.249 3294 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.37 % Allowed : 16.87 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.33), residues: 665 helix: 2.04 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.25 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 79 TYR 0.048 0.002 TYR D 83 PHE 0.011 0.002 PHE D 70 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (10751) covalent geometry : angle 0.60710 / 0.35 (15498) hydrogen bonds : bond 0.06603 / 4.39 ( 632) hydrogen bonds : angle 2.95291 / 2.08 ( 1605) link_NAG-SER : bond 0.00561 / 0.29 ( 2) link_NAG-SER : angle 3.73012 / 1.85 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.272 Fit side-chains REVERT: C 95 LYS cc_start: 0.7775 (tptt) cc_final: 0.7268 (ttmm) REVERT: D 46 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8125 (ttmt) REVERT: D 62 MET cc_start: 0.8914 (mmm) cc_final: 0.8504 (mmm) REVERT: E 83 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8139 (mtp-110) REVERT: E 134 ARG cc_start: 0.6960 (ptm-80) cc_final: 0.6525 (tpp80) REVERT: F 25 ASN cc_start: 0.8066 (t160) cc_final: 0.7676 (t0) REVERT: F 27 GLN cc_start: 0.8618 (mp10) cc_final: 0.8120 (tm-30) REVERT: H 120 LYS cc_start: 0.8653 (mttm) cc_final: 0.8369 (tttp) outliers start: 19 outliers final: 14 residues processed: 145 average time/residue: 0.1087 time to fit residues: 21.2997 Evaluate side-chains 138 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 50.0000 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 73 optimal weight: 50.0000 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 84 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.150769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.105320 restraints weight = 21261.205| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.30 r_work: 0.3278 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10753 Z= 0.131 Angle : 0.585 9.202 15502 Z= 0.341 Chirality : 0.040 0.344 1776 Planarity : 0.004 0.034 1161 Dihedral : 30.821 177.512 3294 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.31 % Allowed : 18.65 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.33), residues: 665 helix: 2.15 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.21 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 79 TYR 0.038 0.002 TYR D 83 PHE 0.011 0.001 PHE D 70 HIS 0.001 0.000 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.13 (10751) covalent geometry : angle 0.58224 / 0.34 (15498) hydrogen bonds : bond 0.06411 / 4.25 ( 632) hydrogen bonds : angle 2.89429 / 2.05 ( 1605) link_NAG-SER : bond 0.00497 / 0.26 ( 2) link_NAG-SER : angle 3.75483 / 1.86 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.290 Fit side-chains REVERT: A 60 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6983 (mt) REVERT: D 46 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8130 (ttmt) REVERT: D 62 MET cc_start: 0.8895 (mmm) cc_final: 0.8484 (mmm) REVERT: E 83 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8154 (mtt-85) REVERT: E 134 ARG cc_start: 0.6928 (ptm-80) cc_final: 0.6498 (tpp80) REVERT: F 27 GLN cc_start: 0.8599 (mp10) cc_final: 0.8064 (tm-30) REVERT: H 120 LYS cc_start: 0.8645 (mttm) cc_final: 0.8321 (tttp) outliers start: 13 outliers final: 11 residues processed: 141 average time/residue: 0.1130 time to fit residues: 21.2609 Evaluate side-chains 137 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN G 84 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.150759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.104370 restraints weight = 21375.636| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.40 r_work: 0.3257 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10753 Z= 0.131 Angle : 0.580 9.269 15502 Z= 0.338 Chirality : 0.040 0.344 1776 Planarity : 0.004 0.035 1161 Dihedral : 30.801 177.790 3294 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.13 % Allowed : 19.01 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.32), residues: 665 helix: 2.20 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.23 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 79 TYR 0.030 0.002 TYR C 57 PHE 0.013 0.001 PHE E 84 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (10751) covalent geometry : angle 0.57723 / 0.34 (15498) hydrogen bonds : bond 0.06393 / 4.24 ( 632) hydrogen bonds : angle 2.88221 / 2.05 ( 1605) link_NAG-SER : bond 0.00512 / 0.26 ( 2) link_NAG-SER : angle 3.85986 / 1.91 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.220 Fit side-chains REVERT: A 60 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7026 (mt) REVERT: D 46 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8102 (ttmt) REVERT: D 62 MET cc_start: 0.8880 (mmm) cc_final: 0.8461 (mmm) REVERT: E 83 ARG cc_start: 0.8548 (mtp85) cc_final: 0.8193 (mtt-85) REVERT: E 134 ARG cc_start: 0.6929 (ptm-80) cc_final: 0.6522 (tpp80) REVERT: F 27 GLN cc_start: 0.8645 (mp10) cc_final: 0.8120 (tm-30) REVERT: G 29 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8083 (ttt180) REVERT: H 120 LYS cc_start: 0.8593 (mttm) cc_final: 0.8265 (tttp) outliers start: 12 outliers final: 11 residues processed: 138 average time/residue: 0.1081 time to fit residues: 19.9981 Evaluate side-chains 137 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN G 38 ASN G 84 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.149543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.102266 restraints weight = 20898.258| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.17 r_work: 0.3259 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10753 Z= 0.160 Angle : 0.605 9.457 15502 Z= 0.347 Chirality : 0.040 0.347 1776 Planarity : 0.004 0.034 1161 Dihedral : 30.839 178.026 3294 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.66 % Allowed : 19.36 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.32), residues: 665 helix: 2.13 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 79 TYR 0.030 0.002 TYR C 57 PHE 0.011 0.001 PHE D 70 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (10751) covalent geometry : angle 0.60227 / 0.35 (15498) hydrogen bonds : bond 0.06437 / 4.27 ( 632) hydrogen bonds : angle 2.92477 / 2.08 ( 1605) link_NAG-SER : bond 0.00464 / 0.24 ( 2) link_NAG-SER : angle 3.75882 / 1.87 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.266 Fit side-chains REVERT: D 46 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8100 (ttmt) REVERT: D 62 MET cc_start: 0.8900 (mmm) cc_final: 0.8471 (mmm) REVERT: E 83 ARG cc_start: 0.8544 (mtp85) cc_final: 0.8143 (mtt-85) REVERT: E 134 ARG cc_start: 0.6887 (ptm-80) cc_final: 0.6459 (tpp80) REVERT: F 27 GLN cc_start: 0.8617 (mp10) cc_final: 0.8092 (tm-30) REVERT: G 84 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8525 (tp40) REVERT: H 36 SER cc_start: 0.7629 (t) cc_final: 0.6886 (m) REVERT: H 120 LYS cc_start: 0.8634 (mttm) cc_final: 0.8336 (tttp) outliers start: 15 outliers final: 14 residues processed: 140 average time/residue: 0.1095 time to fit residues: 20.6825 Evaluate side-chains 143 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 51 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.150528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.103761 restraints weight = 21069.615| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.34 r_work: 0.3274 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10753 Z= 0.128 Angle : 0.584 9.190 15502 Z= 0.340 Chirality : 0.040 0.342 1776 Planarity : 0.004 0.037 1161 Dihedral : 30.804 177.635 3294 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.66 % Allowed : 19.18 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.32), residues: 665 helix: 2.23 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 79 TYR 0.027 0.002 TYR C 57 PHE 0.012 0.001 PHE D 70 HIS 0.001 0.000 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.13 (10751) covalent geometry : angle 0.58037 / 0.34 (15498) hydrogen bonds : bond 0.06318 / 4.19 ( 632) hydrogen bonds : angle 2.85770 / 2.03 ( 1605) link_NAG-SER : bond 0.00497 / 0.26 ( 2) link_NAG-SER : angle 3.89973 / 1.95 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2157.99 seconds wall clock time: 37 minutes 29.85 seconds (2249.85 seconds total)