Starting phenix.real_space_refine on Wed Aug 5 13:33:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3q_46544/08_2026/9d3q_46544.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3q_46544/08_2026/9d3q_46544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d3q_46544/08_2026/9d3q_46544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3q_46544/08_2026/9d3q_46544.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3q_46544/08_2026/9d3q_46544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3q_46544/08_2026/9d3q_46544.map" } resolution = 2.8 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= 0.001 sd= 0.049 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 218 5.49 5 S 14 5.16 5 C 5676 2.51 5 N 1903 2.21 5 O 2327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 10138 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 636 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 729 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 730 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} 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: "F" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 700 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 88} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 709 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2251 Classifications: {'DNA': 109} Link IDs: {'rna3p': 108} Chain: "J" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2218 Classifications: {'DNA': 109} Link IDs: {'rna3p': 108} Time building chain proxies: 1.81, per 1000 atoms: 0.18 Number of scatterers: 10138 At special positions: 0 Unit cell: (116.875, 77.605, 115.94, 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 218 15.00 O 2327 8.00 N 1903 7.00 C 5676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 163.5 milliseconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 74.8% alpha, 3.3% beta 108 base pairs and 193 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 4.398A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.920A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.638A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 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 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.938A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 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: 3.847A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 20 removed outlier: 3.585A pdb=" N ARG G 20 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.579A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.651A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.537A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.164A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.529A pdb=" N THR B 96 " --> 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: 7.442A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.761A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.817A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.528A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 397 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 283 hydrogen bonds 566 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 193 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2135 1.33 - 1.45: 3204 1.45 - 1.57: 4953 1.57 - 1.69: 434 1.69 - 1.81: 26 Bond restraints: 10752 Sorted by residual: bond pdb=" C3' DG I 49 " pdb=" C2' DG I 49 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.95e+00 bond pdb=" C3' DC I 41 " pdb=" C2' DC I 41 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.23e+00 bond pdb=" C3' DG I 19 " pdb=" C2' DG I 19 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.16e+00 bond pdb=" C3' DC J -14 " pdb=" C2' DC J -14 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.02e+00 ... (remaining 10747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 14215 1.37 - 2.73: 1132 2.73 - 4.10: 77 4.10 - 5.47: 11 5.47 - 6.84: 6 Bond angle restraints: 15441 Sorted by residual: angle pdb=" N ARG G 20 " pdb=" CA ARG G 20 " pdb=" C ARG G 20 " ideal model delta sigma weight residual 114.56 107.72 6.84 1.27e+00 6.20e-01 2.90e+01 angle pdb=" N3 DT J 49 " pdb=" C4 DT J 49 " pdb=" O4 DT J 49 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT J 39 " pdb=" C4 DT J 39 " pdb=" O4 DT J 39 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 15436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.95: 4688 34.95 - 69.89: 1165 69.89 - 104.84: 29 104.84 - 139.79: 1 139.79 - 174.73: 1 Dihedral angle restraints: 5884 sinusoidal: 3801 harmonic: 2083 Sorted by residual: dihedral pdb=" C4' DA J -17 " pdb=" C3' DA J -17 " pdb=" O3' DA J -17 " pdb=" P DG J -16 " ideal model delta sinusoidal sigma weight residual -140.00 34.73 -174.73 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 91.08 128.92 1 3.50e+01 8.16e-04 1.28e+01 dihedral pdb=" CG ARG C 32 " pdb=" CD ARG C 32 " pdb=" NE ARG C 32 " pdb=" CZ ARG C 32 " ideal model delta sinusoidal sigma weight residual 180.00 135.07 44.93 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 5881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 847 0.027 - 0.054: 582 0.054 - 0.081: 205 0.081 - 0.108: 91 0.108 - 0.135: 33 Chirality restraints: 1758 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE D 89 " pdb=" N ILE D 89 " pdb=" C ILE D 89 " pdb=" CB ILE D 89 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1755 not shown) Planarity restraints: 1202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO G 80 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " 0.025 2.00e-02 2.50e+03 1.02e-02 3.14e+00 pdb=" N9 DG I -35 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 17 " 0.022 2.00e-02 2.50e+03 1.11e-02 3.09e+00 pdb=" N1 DT I 17 " -0.023 2.00e-02 2.50e+03 pdb=" C2 DT I 17 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 17 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 17 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 17 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT I 17 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 17 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 17 " 0.002 2.00e-02 2.50e+03 ... (remaining 1199 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1991 2.79 - 3.32: 8860 3.32 - 3.84: 20015 3.84 - 4.37: 23604 4.37 - 4.90: 34283 Nonbonded interactions: 88753 Sorted by model distance: nonbonded pdb=" N2 DG I 49 " pdb=" O2 DT J -48 " model vdw 2.260 3.120 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR D 42 " pdb=" O5' DG I -53 " model vdw 2.326 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.345 3.120 nonbonded pdb=" O THR G 76 " pdb=" OG1 THR G 76 " model vdw 2.347 3.040 ... (remaining 88748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 43 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 22 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 101 or (resid 102 and (name N or name CA or na \ me C or name O )))) } ncs_group { reference = (chain 'C' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 or (resid 17 and (name N or name CA or name C or name O or name C \ B )) or resid 18 through 106)) selection = chain 'G' } ncs_group { reference = (chain 'D' and ((resid 33 through 34 and (name N or name CA or name C or name O \ or name CB )) or resid 35 through 124)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.790 Find NCS groups from input model: 0.090 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:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10752 Z= 0.486 Angle : 0.748 6.836 15441 Z= 0.657 Chirality : 0.043 0.135 1758 Planarity : 0.004 0.053 1202 Dihedral : 28.637 174.732 4544 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.55 % Allowed : 26.53 % Favored : 70.92 % 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: 1.60 (0.31), residues: 706 helix: 1.68 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -0.86 (0.41), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 35 TYR 0.010 0.001 TYR C 57 PHE 0.012 0.001 PHE B 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.49 (10752) covalent geometry : angle 0.74760 / 0.66 (15441) hydrogen bonds : bond 0.10039 / 6.51 ( 680) hydrogen bonds : angle 4.06308 / 2.94 ( 1742) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.258 Fit side-chains REVERT: A 112 ILE cc_start: 0.8972 (mm) cc_final: 0.8729 (mt) REVERT: C 77 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.6921 (mtt90) REVERT: F 44 LYS cc_start: 0.8776 (tptp) cc_final: 0.8536 (tptp) outliers start: 15 outliers final: 12 residues processed: 95 average time/residue: 0.7400 time to fit residues: 74.2418 Evaluate side-chains 85 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.192180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132417 restraints weight = 11647.771| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.39 r_work: 0.3487 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10752 Z= 0.195 Angle : 0.657 7.518 15441 Z= 0.383 Chirality : 0.047 0.244 1758 Planarity : 0.005 0.054 1202 Dihedral : 30.764 169.726 3177 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.27 % Allowed : 24.83 % Favored : 69.90 % 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: 1.63 (0.31), residues: 706 helix: 1.72 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.06 (0.41), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 35 TYR 0.011 0.002 TYR C 57 PHE 0.015 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (10752) covalent geometry : angle 0.65657 / 0.38 (15441) hydrogen bonds : bond 0.05311 / 3.54 ( 680) hydrogen bonds : angle 3.24559 / 2.34 ( 1742) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.203 Fit side-chains REVERT: A 76 GLN cc_start: 0.8288 (tp40) cc_final: 0.8055 (tp40) REVERT: B 44 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7914 (mtmt) REVERT: B 79 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7711 (mtmt) REVERT: C 24 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: C 77 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.6928 (mtt90) REVERT: D 93 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: H 108 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7828 (tttm) outliers start: 31 outliers final: 15 residues processed: 101 average time/residue: 0.8342 time to fit residues: 88.5310 Evaluate side-chains 91 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 78 optimal weight: 30.0000 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.192514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132733 restraints weight = 11686.785| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.40 r_work: 0.3496 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10752 Z= 0.176 Angle : 0.635 7.503 15441 Z= 0.369 Chirality : 0.046 0.239 1758 Planarity : 0.005 0.063 1202 Dihedral : 30.890 170.217 3171 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.74 % Allowed : 26.02 % Favored : 70.24 % 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: 1.82 (0.31), residues: 706 helix: 1.86 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.01 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.011 0.001 TYR C 57 PHE 0.010 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 (10752) covalent geometry : angle 0.63518 / 0.37 (15441) hydrogen bonds : bond 0.04977 / 3.32 ( 680) hydrogen bonds : angle 3.14115 / 2.27 ( 1742) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.290 Fit side-chains REVERT: B 44 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7919 (mtmt) REVERT: C 24 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: C 77 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.6982 (mtt90) REVERT: D 93 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: F 35 ARG cc_start: 0.8447 (mtp-110) cc_final: 0.8140 (mtm110) REVERT: G 71 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6663 (ttp-110) REVERT: H 108 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7785 (tttm) outliers start: 22 outliers final: 12 residues processed: 88 average time/residue: 0.7714 time to fit residues: 71.2623 Evaluate side-chains 88 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 85 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.191028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131037 restraints weight = 11850.090| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.41 r_work: 0.3475 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10752 Z= 0.190 Angle : 0.643 7.909 15441 Z= 0.369 Chirality : 0.046 0.244 1758 Planarity : 0.005 0.054 1202 Dihedral : 31.095 169.160 3168 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.25 % Allowed : 25.68 % Favored : 70.07 % 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 (0.31), residues: 706 helix: 1.93 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.04 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.011 0.001 TYR C 57 PHE 0.013 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (10752) covalent geometry : angle 0.64282 / 0.37 (15441) hydrogen bonds : bond 0.05017 / 3.34 ( 680) hydrogen bonds : angle 3.09355 / 2.24 ( 1742) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.242 Fit side-chains REVERT: B 44 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7945 (mtmt) REVERT: B 79 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7738 (mtmt) REVERT: C 24 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7079 (mp10) REVERT: C 77 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.6934 (mtt90) REVERT: D 93 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: F 35 ARG cc_start: 0.8413 (mtp-110) cc_final: 0.8074 (mtm110) REVERT: G 92 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: H 108 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7703 (tttm) outliers start: 25 outliers final: 15 residues processed: 98 average time/residue: 0.7326 time to fit residues: 75.3664 Evaluate side-chains 96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.192682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133052 restraints weight = 11689.448| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.41 r_work: 0.3509 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10752 Z= 0.141 Angle : 0.613 7.461 15441 Z= 0.355 Chirality : 0.045 0.240 1758 Planarity : 0.004 0.053 1202 Dihedral : 31.086 169.704 3168 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.08 % Allowed : 26.36 % Favored : 69.56 % 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: 2.24 (0.31), residues: 706 helix: 2.19 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.92 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 79 TYR 0.010 0.001 TYR C 57 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (10752) covalent geometry : angle 0.61261 / 0.35 (15441) hydrogen bonds : bond 0.04525 / 3.02 ( 680) hydrogen bonds : angle 2.99945 / 2.17 ( 1742) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.194 Fit side-chains REVERT: B 44 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7950 (mtmt) REVERT: B 49 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8231 (mt) REVERT: C 24 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7076 (mp10) REVERT: C 77 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.6952 (mtt90) REVERT: D 93 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: F 35 ARG cc_start: 0.8415 (mtp-110) cc_final: 0.8130 (mtm110) REVERT: G 92 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: H 108 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7701 (tttm) outliers start: 24 outliers final: 14 residues processed: 90 average time/residue: 0.8556 time to fit residues: 80.8459 Evaluate side-chains 93 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.192882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132967 restraints weight = 11999.440| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.42 r_work: 0.3510 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10752 Z= 0.139 Angle : 0.603 7.226 15441 Z= 0.351 Chirality : 0.044 0.239 1758 Planarity : 0.004 0.053 1202 Dihedral : 31.075 169.837 3166 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.91 % Allowed : 27.04 % Favored : 69.05 % 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: 2.40 (0.32), residues: 706 helix: 2.31 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.85 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.009 0.001 TYR C 57 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (10752) covalent geometry : angle 0.60311 / 0.35 (15441) hydrogen bonds : bond 0.04420 / 2.95 ( 680) hydrogen bonds : angle 2.95561 / 2.14 ( 1742) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.274 Fit side-chains REVERT: A 122 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8167 (mtmt) REVERT: B 44 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7945 (mtmt) REVERT: B 49 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8219 (mt) REVERT: C 24 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7019 (mp10) REVERT: C 77 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.6889 (mtt90) REVERT: D 93 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: F 35 ARG cc_start: 0.8419 (mtp-110) cc_final: 0.8105 (mtm110) REVERT: H 108 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7600 (tttm) outliers start: 23 outliers final: 12 residues processed: 92 average time/residue: 0.7942 time to fit residues: 76.7020 Evaluate side-chains 91 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.189922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130120 restraints weight = 11634.679| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.39 r_work: 0.3465 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10752 Z= 0.209 Angle : 0.659 8.053 15441 Z= 0.373 Chirality : 0.047 0.248 1758 Planarity : 0.005 0.054 1202 Dihedral : 31.182 168.211 3166 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.59 % Allowed : 26.70 % Favored : 68.71 % 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: 1.94 (0.31), residues: 706 helix: 1.98 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.05 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 79 TYR 0.012 0.002 TYR C 57 PHE 0.017 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (10752) covalent geometry : angle 0.65886 / 0.37 (15441) hydrogen bonds : bond 0.05249 / 3.49 ( 680) hydrogen bonds : angle 3.10745 / 2.24 ( 1742) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.256 Fit side-chains REVERT: A 133 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: B 44 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7975 (mtmt) REVERT: C 24 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: C 77 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.6977 (mtt90) REVERT: D 93 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: F 35 ARG cc_start: 0.8457 (mtp-110) cc_final: 0.8100 (mtm110) REVERT: G 71 ARG cc_start: 0.7813 (ttp-110) cc_final: 0.7602 (ttp-110) REVERT: G 92 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: H 108 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7670 (tttp) outliers start: 27 outliers final: 16 residues processed: 96 average time/residue: 0.8401 time to fit residues: 84.4950 Evaluate side-chains 95 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 75 HIS D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.191637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.132107 restraints weight = 11680.720| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.40 r_work: 0.3500 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10752 Z= 0.138 Angle : 0.633 12.003 15441 Z= 0.361 Chirality : 0.045 0.243 1758 Planarity : 0.004 0.054 1202 Dihedral : 31.195 168.827 3165 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.57 % Allowed : 27.89 % Favored : 68.54 % 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: 2.17 (0.31), residues: 706 helix: 2.15 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.96 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 79 TYR 0.011 0.001 TYR C 57 PHE 0.012 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (10752) covalent geometry : angle 0.63254 / 0.36 (15441) hydrogen bonds : bond 0.04699 / 3.13 ( 680) hydrogen bonds : angle 3.03843 / 2.20 ( 1742) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.274 Fit side-chains REVERT: A 133 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: B 44 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7823 (mttp) REVERT: C 24 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7082 (mp10) REVERT: C 77 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.6975 (mtt90) REVERT: D 93 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: F 35 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.8114 (mtm110) REVERT: G 92 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: H 108 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7661 (tttp) outliers start: 21 outliers final: 15 residues processed: 90 average time/residue: 0.8173 time to fit residues: 77.2308 Evaluate side-chains 94 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.191394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131847 restraints weight = 11655.049| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.39 r_work: 0.3497 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10752 Z= 0.155 Angle : 0.632 13.734 15441 Z= 0.359 Chirality : 0.045 0.244 1758 Planarity : 0.004 0.053 1202 Dihedral : 31.190 168.760 3165 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.74 % Allowed : 27.72 % Favored : 68.54 % 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 (0.31), residues: 706 helix: 2.18 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.95 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.011 0.001 TYR C 57 PHE 0.012 0.001 PHE E 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (10752) covalent geometry : angle 0.63207 / 0.36 (15441) hydrogen bonds : bond 0.04692 / 3.13 ( 680) hydrogen bonds : angle 3.03250 / 2.19 ( 1742) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.267 Fit side-chains REVERT: A 133 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: B 44 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.7810 (mttp) REVERT: C 24 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7063 (mp10) REVERT: C 77 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.6919 (mtt90) REVERT: D 93 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: F 35 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.8064 (mtm110) REVERT: G 92 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: H 108 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7630 (tttp) outliers start: 22 outliers final: 15 residues processed: 87 average time/residue: 0.8397 time to fit residues: 76.6764 Evaluate side-chains 92 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 78 optimal weight: 30.0000 chunk 41 optimal weight: 0.7980 chunk 80 optimal weight: 50.0000 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 30.0000 chunk 89 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.191577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132124 restraints weight = 11531.489| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.39 r_work: 0.3502 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10752 Z= 0.152 Angle : 0.634 16.292 15441 Z= 0.359 Chirality : 0.045 0.243 1758 Planarity : 0.004 0.053 1202 Dihedral : 31.186 168.847 3165 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.57 % Allowed : 27.89 % Favored : 68.54 % 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: 2.24 (0.31), residues: 706 helix: 2.21 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.93 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.010 0.001 TYR C 57 PHE 0.011 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (10752) covalent geometry : angle 0.63411 / 0.36 (15441) hydrogen bonds : bond 0.04631 / 3.09 ( 680) hydrogen bonds : angle 3.02208 / 2.18 ( 1742) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.293 Fit side-chains REVERT: A 133 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: B 44 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7808 (mttp) REVERT: C 24 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: C 77 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.6917 (mtt90) REVERT: D 93 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: F 35 ARG cc_start: 0.8389 (mtp-110) cc_final: 0.8054 (mtm110) REVERT: G 92 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: H 108 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7605 (tttp) outliers start: 21 outliers final: 14 residues processed: 90 average time/residue: 0.8778 time to fit residues: 82.9023 Evaluate side-chains 94 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 0.0470 chunk 65 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.192055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132345 restraints weight = 11838.603| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.41 r_work: 0.3506 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10752 Z= 0.134 Angle : 0.630 18.759 15441 Z= 0.356 Chirality : 0.044 0.242 1758 Planarity : 0.004 0.053 1202 Dihedral : 31.183 169.123 3161 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.40 % Allowed : 27.72 % Favored : 68.88 % 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: 2.36 (0.31), residues: 706 helix: 2.30 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.89 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.010 0.001 TYR C 57 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (10752) covalent geometry : angle 0.62970 / 0.36 (15441) hydrogen bonds : bond 0.04488 / 3.00 ( 680) hydrogen bonds : angle 2.99758 / 2.16 ( 1742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3477.56 seconds wall clock time: 59 minutes 41.84 seconds (3581.84 seconds total)