Starting phenix.real_space_refine on Thu Jul 2 20:07:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xsf_67179/07_2026/9xsf_67179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xsf_67179/07_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_67179/07_2026/9xsf_67179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xsf_67179/07_2026/9xsf_67179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xsf_67179/07_2026/9xsf_67179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xsf_67179/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.33, per 1000 atoms: 0.23 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: 1.02 Conformation dependent library (CDL) restraints added in 221.6 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: 1.48 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: 1.84 Time building geometry restraints manager: 1.32 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: 13923 1.13 - 2.26: 1115 2.26 - 3.39: 416 3.39 - 4.53: 35 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: 1.260 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.630 Find NCS groups from input model: 0.130 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- 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= 0.492 Angle : 0.755 8.789 15502 Z= 0.638 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 0.75140 / 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 : 0.276 Fit side-chains REVERT: D 108 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7423 (ptpt) REVERT: D 120 LYS cc_start: 0.8222 (mttm) cc_final: 0.7975 (mttt) 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: 0.7684 (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: 0.1582 time to fit residues: 31.9446 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 : 0.267 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.154775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.111842 restraints weight = 22075.403| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.10 r_work: 0.3437 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1595 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= 0.157 Angle : 0.628 7.866 15502 Z= 0.377 Chirality : 0.043 0.297 1776 Planarity : 0.005 0.043 1161 Dihedral : 30.663 179.456 3294 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 2.66 % Allowed : 8.88 % Favored : 88.45 % 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 (0.33), residues: 665 helix: 1.78 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.68 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 35 TYR 0.010 0.001 TYR G 50 PHE 0.007 0.002 PHE H 70 HIS 0.006 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.16 (10751) covalent geometry : angle 0.62427 / 0.38 (15498) hydrogen bonds : bond 0.07939 / 5.16 ( 632) hydrogen bonds : angle 3.59248 / 2.48 ( 1605) link_NAG-SER : bond 0.00809 / 0.42 ( 2) link_NAG-SER : angle 4.52993 / 2.27 ( 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 144 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.340 Fit side-chains REVERT: D 108 LYS cc_start: 0.7793 (mmmt) cc_final: 0.7402 (ptpt) REVERT: D 120 LYS cc_start: 0.8142 (mttm) cc_final: 0.7818 (mttt) REVERT: E 83 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.8091 (mtp-110) REVERT: E 134 ARG cc_start: 0.6855 (ptm-80) cc_final: 0.6467 (tpp80) REVERT: F 27 GLN cc_start: 0.8587 (mp10) cc_final: 0.8021 (tm-30) REVERT: H 120 LYS cc_start: 0.8643 (mttm) cc_final: 0.8201 (mtpt) outliers start: 15 outliers final: 11 residues processed: 134 average time/residue: 0.1207 time to fit residues: 21.5429 Evaluate side-chains 123 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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: 0.8980 chunk 7 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 45 optimal weight: 0.0670 chunk 22 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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** D 82 HIS F 25 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.153518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.110473 restraints weight = 22265.132| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.26 r_work: 0.3396 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10753 Z= 0.155 Angle : 0.596 8.264 15502 Z= 0.357 Chirality : 0.042 0.313 1776 Planarity : 0.004 0.033 1161 Dihedral : 30.807 179.201 3294 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.49 % Allowed : 11.55 % Favored : 85.97 % 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: 1.88 (0.33), residues: 665 helix: 2.00 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.45 (0.46), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 79 TYR 0.024 0.002 TYR D 83 PHE 0.034 0.002 PHE E 84 HIS 0.004 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (10751) covalent geometry : angle 0.59146 / 0.36 (15498) hydrogen bonds : bond 0.07097 / 4.69 ( 632) hydrogen bonds : angle 3.19055 / 2.22 ( 1605) link_NAG-SER : bond 0.00773 / 0.40 ( 2) link_NAG-SER : angle 4.49924 / 2.20 ( 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 139 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.278 Fit side-chains REVERT: C 64 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7916 (tm-30) REVERT: D 46 LYS cc_start: 0.8504 (ttmm) cc_final: 0.8272 (ttmt) REVERT: D 108 LYS cc_start: 0.7694 (mmmt) cc_final: 0.7418 (ptpt) REVERT: D 120 LYS cc_start: 0.8009 (mttm) cc_final: 0.7729 (mttt) REVERT: E 83 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.8255 (mtt-85) REVERT: E 97 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: E 134 ARG cc_start: 0.7000 (ptm-80) cc_final: 0.6359 (tpp80) REVERT: F 27 GLN cc_start: 0.8616 (mp10) cc_final: 0.8110 (tm-30) REVERT: H 120 LYS cc_start: 0.8601 (mttm) cc_final: 0.8133 (mtpt) outliers start: 14 outliers final: 7 residues processed: 133 average time/residue: 0.1268 time to fit residues: 22.3817 Evaluate side-chains 119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 31 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 50.0000 chunk 60 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 85 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.152460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.108689 restraints weight = 21480.521| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.69 r_work: 0.3316 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10753 Z= 0.135 Angle : 0.572 8.341 15502 Z= 0.343 Chirality : 0.041 0.314 1776 Planarity : 0.004 0.043 1161 Dihedral : 30.847 177.903 3294 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.55 % Allowed : 12.79 % Favored : 83.66 % 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: 2.13 (0.33), residues: 665 helix: 2.16 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.31 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 79 TYR 0.033 0.002 TYR D 83 PHE 0.007 0.001 PHE D 70 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (10751) covalent geometry : angle 0.56867 / 0.34 (15498) hydrogen bonds : bond 0.06830 / 4.53 ( 632) hydrogen bonds : angle 2.99503 / 2.11 ( 1605) link_NAG-SER : bond 0.00604 / 0.31 ( 2) link_NAG-SER : angle 4.10590 / 2.00 ( 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 145 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7640 (tptt) cc_final: 0.7181 (ttmm) REVERT: D 46 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8211 (ttmt) REVERT: D 108 LYS cc_start: 0.7574 (mmmt) cc_final: 0.7373 (ptpt) REVERT: D 120 LYS cc_start: 0.8007 (mttm) cc_final: 0.7699 (mttt) REVERT: E 83 ARG cc_start: 0.8514 (mtt-85) cc_final: 0.8267 (mtt-85) REVERT: E 134 ARG cc_start: 0.7019 (ptm-80) cc_final: 0.6323 (tpp80) REVERT: F 27 GLN cc_start: 0.8627 (mp10) cc_final: 0.8065 (tm-30) REVERT: G 95 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7611 (ttmm) REVERT: H 120 LYS cc_start: 0.8635 (mttm) cc_final: 0.8171 (tttp) outliers start: 20 outliers final: 7 residues processed: 134 average time/residue: 0.1054 time to fit residues: 18.8814 Evaluate side-chains 127 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 95 LYS 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: 4.9990 chunk 74 optimal weight: 50.0000 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 overall best weight: 1.2962 ------------------------------------------------------------------------------- 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 63 ASN H 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.150855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104092 restraints weight = 21142.867| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.28 r_work: 0.3290 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10753 Z= 0.150 Angle : 0.584 8.702 15502 Z= 0.344 Chirality : 0.040 0.320 1776 Planarity : 0.005 0.066 1161 Dihedral : 30.922 178.069 3294 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.37 % Allowed : 14.74 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.33), residues: 665 helix: 2.16 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.31 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 79 TYR 0.028 0.002 TYR D 83 PHE 0.009 0.001 PHE E 84 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (10751) covalent geometry : angle 0.58067 / 0.34 (15498) hydrogen bonds : bond 0.06713 / 4.46 ( 632) hydrogen bonds : angle 2.95165 / 2.08 ( 1605) link_NAG-SER : bond 0.00618 / 0.32 ( 2) link_NAG-SER : angle 3.81642 / 1.87 ( 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 144 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.265 Fit side-chains REVERT: C 95 LYS cc_start: 0.7695 (tptt) cc_final: 0.7223 (ttmm) REVERT: D 46 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8158 (ttmt) REVERT: D 62 MET cc_start: 0.8805 (mmm) cc_final: 0.8469 (mmm) REVERT: E 83 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.8351 (mtt-85) REVERT: E 134 ARG cc_start: 0.7037 (ptm-80) cc_final: 0.6353 (tpp80) REVERT: F 27 GLN cc_start: 0.8620 (mp10) cc_final: 0.8074 (tm-30) REVERT: G 95 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7703 (ttmm) REVERT: H 120 LYS cc_start: 0.8668 (mttm) cc_final: 0.8253 (tttp) REVERT: H 121 TYR cc_start: 0.8610 (t80) cc_final: 0.8108 (t80) outliers start: 19 outliers final: 11 residues processed: 136 average time/residue: 0.1113 time to fit residues: 20.4043 Evaluate side-chains 131 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 95 LYS 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: 0.9990 chunk 67 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.151145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.104974 restraints weight = 21358.590| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.22 r_work: 0.3315 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2884 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= 0.134 Angle : 0.571 8.607 15502 Z= 0.339 Chirality : 0.040 0.319 1776 Planarity : 0.004 0.049 1161 Dihedral : 30.908 177.485 3294 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.84 % Allowed : 16.34 % 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: 2.20 (0.33), residues: 665 helix: 2.21 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.26 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.018 0.001 TYR D 83 PHE 0.008 0.001 PHE E 84 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (10751) covalent geometry : angle 0.56811 / 0.34 (15498) hydrogen bonds : bond 0.06589 / 4.37 ( 632) hydrogen bonds : angle 2.89504 / 2.04 ( 1605) link_NAG-SER : bond 0.00585 / 0.30 ( 2) link_NAG-SER : angle 3.63428 / 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 140 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.172 Fit side-chains REVERT: C 95 LYS cc_start: 0.7675 (tptt) cc_final: 0.7160 (ttmm) REVERT: D 46 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8131 (ttmt) REVERT: D 62 MET cc_start: 0.8820 (mmm) cc_final: 0.8411 (mmm) REVERT: E 83 ARG cc_start: 0.8598 (mtt-85) cc_final: 0.8310 (mtt-85) REVERT: E 134 ARG cc_start: 0.7012 (ptm-80) cc_final: 0.6468 (tpp80) REVERT: F 27 GLN cc_start: 0.8633 (mp10) cc_final: 0.8068 (tm-30) REVERT: G 95 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7632 (ttmm) REVERT: H 120 LYS cc_start: 0.8588 (mttm) cc_final: 0.8253 (tttp) outliers start: 16 outliers final: 12 residues processed: 134 average time/residue: 0.1102 time to fit residues: 19.7764 Evaluate side-chains 131 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 76 GLN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 95 LYS 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: 50.0000 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 50.0000 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.150829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104429 restraints weight = 21188.410| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.45 r_work: 0.3274 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10753 Z= 0.140 Angle : 0.573 8.741 15502 Z= 0.338 Chirality : 0.040 0.322 1776 Planarity : 0.004 0.035 1161 Dihedral : 30.913 177.550 3294 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.91 % Allowed : 15.99 % Favored : 80.11 % 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 : -1.27 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 79 TYR 0.022 0.002 TYR D 83 PHE 0.007 0.001 PHE F 100 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (10751) covalent geometry : angle 0.56981 / 0.34 (15498) hydrogen bonds : bond 0.06526 / 4.34 ( 632) hydrogen bonds : angle 2.88206 / 2.03 ( 1605) link_NAG-SER : bond 0.00556 / 0.29 ( 2) link_NAG-SER : angle 3.72540 / 1.84 ( 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 152 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.333 Fit side-chains REVERT: C 95 LYS cc_start: 0.7742 (tptt) cc_final: 0.7231 (ttmm) REVERT: D 46 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8126 (ttmt) REVERT: D 62 MET cc_start: 0.8871 (mmm) cc_final: 0.8472 (mmm) REVERT: E 134 ARG cc_start: 0.6988 (ptm-80) cc_final: 0.6489 (tpp80) REVERT: F 27 GLN cc_start: 0.8650 (mp10) cc_final: 0.8095 (tm-30) REVERT: G 95 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7713 (ttmm) REVERT: H 120 LYS cc_start: 0.8636 (mttm) cc_final: 0.8332 (tttp) outliers start: 22 outliers final: 13 residues processed: 143 average time/residue: 0.1157 time to fit residues: 22.6285 Evaluate side-chains 134 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 D residue 39 VAL Chi-restraints excluded: chain E residue 87 SER 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 95 LYS 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: 0.9990 chunk 74 optimal weight: 50.0000 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 73 optimal weight: 50.0000 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 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 F 25 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.151339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.105747 restraints weight = 21273.091| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.36 r_work: 0.3292 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10753 Z= 0.131 Angle : 0.571 8.631 15502 Z= 0.338 Chirality : 0.040 0.320 1776 Planarity : 0.004 0.035 1161 Dihedral : 30.853 177.242 3294 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.66 % Allowed : 18.29 % 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: 2.30 (0.33), residues: 665 helix: 2.28 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.22 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 79 TYR 0.048 0.002 TYR H 83 PHE 0.008 0.001 PHE D 70 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.13 (10751) covalent geometry : angle 0.56820 / 0.34 (15498) hydrogen bonds : bond 0.06425 / 4.26 ( 632) hydrogen bonds : angle 2.87373 / 2.04 ( 1605) link_NAG-SER : bond 0.00527 / 0.27 ( 2) link_NAG-SER : angle 3.75515 / 1.84 ( 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 149 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.276 Fit side-chains REVERT: C 95 LYS cc_start: 0.7698 (tptt) cc_final: 0.7195 (ttmm) REVERT: D 46 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8108 (ttmt) REVERT: D 62 MET cc_start: 0.8849 (mmm) cc_final: 0.8423 (mmm) REVERT: E 134 ARG cc_start: 0.6979 (ptm-80) cc_final: 0.6480 (tpp80) REVERT: F 27 GLN cc_start: 0.8603 (mp10) cc_final: 0.8152 (tm-30) REVERT: G 95 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7711 (ttmm) REVERT: H 36 SER cc_start: 0.7644 (t) cc_final: 0.7088 (m) REVERT: H 120 LYS cc_start: 0.8634 (mttm) cc_final: 0.8356 (tttp) outliers start: 15 outliers final: 11 residues processed: 143 average time/residue: 0.1151 time to fit residues: 22.1815 Evaluate side-chains 134 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 95 LYS 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: 9.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 31 optimal weight: 0.4980 chunk 69 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN G 24 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.151478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.105214 restraints weight = 21342.108| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.42 r_work: 0.3293 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10753 Z= 0.129 Angle : 0.569 8.636 15502 Z= 0.337 Chirality : 0.040 0.319 1776 Planarity : 0.004 0.039 1161 Dihedral : 30.818 177.354 3294 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.84 % Allowed : 19.18 % 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: 2.42 (0.33), residues: 665 helix: 2.37 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.21 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 79 TYR 0.039 0.002 TYR H 83 PHE 0.008 0.001 PHE D 70 HIS 0.002 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.13 (10751) covalent geometry : angle 0.56543 / 0.34 (15498) hydrogen bonds : bond 0.06366 / 4.23 ( 632) hydrogen bonds : angle 2.82896 / 2.01 ( 1605) link_NAG-SER : bond 0.00557 / 0.29 ( 2) link_NAG-SER : angle 3.78909 / 1.88 ( 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 145 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.167 Fit side-chains REVERT: C 61 GLU cc_start: 0.8366 (tp30) cc_final: 0.8152 (tm-30) REVERT: C 95 LYS cc_start: 0.7700 (tptt) cc_final: 0.7231 (ttmm) REVERT: D 40 TYR cc_start: 0.8132 (m-80) cc_final: 0.7704 (m-10) REVERT: D 46 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8099 (ttmt) REVERT: D 62 MET cc_start: 0.8830 (mmm) cc_final: 0.8409 (mmm) REVERT: E 134 ARG cc_start: 0.6926 (ptm-80) cc_final: 0.6476 (tpp80) REVERT: F 27 GLN cc_start: 0.8534 (mp10) cc_final: 0.8071 (tm-30) REVERT: G 95 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7736 (ttmm) REVERT: H 36 SER cc_start: 0.7571 (t) cc_final: 0.7008 (m) REVERT: H 120 LYS cc_start: 0.8623 (mttm) cc_final: 0.8356 (tttp) outliers start: 16 outliers final: 14 residues processed: 139 average time/residue: 0.1089 time to fit residues: 20.3738 Evaluate side-chains 136 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 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 95 LYS 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 32 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 56 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.151277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.104215 restraints weight = 21119.252| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.21 r_work: 0.3306 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 10753 Z= 0.203 Angle : 1.001 59.199 15502 Z= 0.625 Chirality : 0.040 0.320 1776 Planarity : 0.004 0.061 1161 Dihedral : 30.815 177.352 3294 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.66 % Allowed : 19.36 % Favored : 77.98 % Cbeta Deviations : 0.16 % 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: 2.36 (0.33), residues: 665 helix: 2.34 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.27 (0.46), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 79 TYR 0.031 0.002 TYR H 83 PHE 0.009 0.001 PHE D 70 HIS 0.002 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 (10751) covalent geometry : angle 0.99975 / 0.62 (15498) hydrogen bonds : bond 0.06388 / 4.24 ( 632) hydrogen bonds : angle 2.82990 / 2.01 ( 1605) link_NAG-SER : bond 0.00496 / 0.25 ( 2) link_NAG-SER : angle 3.72302 / 1.86 ( 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 138 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.261 Fit side-chains REVERT: C 61 GLU cc_start: 0.8346 (tp30) cc_final: 0.8141 (tm-30) REVERT: C 95 LYS cc_start: 0.7697 (tptt) cc_final: 0.7238 (ttmm) REVERT: D 40 TYR cc_start: 0.8134 (m-80) cc_final: 0.7687 (m-10) REVERT: D 46 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8107 (ttmt) REVERT: D 62 MET cc_start: 0.8838 (mmm) cc_final: 0.8407 (mmm) REVERT: E 134 ARG cc_start: 0.6917 (ptm-80) cc_final: 0.6485 (tpp80) REVERT: F 27 GLN cc_start: 0.8515 (mp10) cc_final: 0.8069 (tm-30) REVERT: G 38 ASN cc_start: 0.8078 (t0) cc_final: 0.7817 (t0) REVERT: G 95 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7735 (ttmm) REVERT: H 36 SER cc_start: 0.7574 (t) cc_final: 0.7003 (m) REVERT: H 120 LYS cc_start: 0.8623 (mttm) cc_final: 0.8372 (tttp) outliers start: 15 outliers final: 14 residues processed: 133 average time/residue: 0.1232 time to fit residues: 21.6996 Evaluate side-chains 137 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 87 SER 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 95 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 14 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 19 optimal weight: 0.0970 chunk 58 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.151214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.104406 restraints weight = 21206.341| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.16 r_work: 0.3312 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 10753 Z= 0.203 Angle : 1.001 59.199 15502 Z= 0.625 Chirality : 0.040 0.320 1776 Planarity : 0.004 0.061 1161 Dihedral : 30.815 177.352 3294 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.66 % Allowed : 19.36 % Favored : 77.98 % Cbeta Deviations : 0.16 % 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: 2.36 (0.33), residues: 665 helix: 2.34 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.27 (0.46), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 79 TYR 0.031 0.002 TYR H 83 PHE 0.009 0.001 PHE D 70 HIS 0.002 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 (10751) covalent geometry : angle 0.99975 / 0.62 (15498) hydrogen bonds : bond 0.06388 / 4.24 ( 632) hydrogen bonds : angle 2.82990 / 2.01 ( 1605) link_NAG-SER : bond 0.00496 / 0.25 ( 2) link_NAG-SER : angle 3.72302 / 1.86 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2275.93 seconds wall clock time: 39 minutes 35.89 seconds (2375.89 seconds total)