Starting phenix.real_space_refine on Thu Jul 2 20:05:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3q_46544/07_2026/9d3q_46544.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3q_46544/07_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_46544/07_2026/9d3q_46544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3q_46544/07_2026/9d3q_46544.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3q_46544/07_2026/9d3q_46544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3q_46544/07_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-dev-6108/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: 1.50, per 1000 atoms: 0.15 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: 0.66 Conformation dependent library (CDL) restraints added in 159.4 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: 1.01 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: 1.43 Time building geometry restraints manager: 0.87 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: 14247 1.37 - 2.73: 1100 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.370 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:5.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.440 ------------------------------------------------------------------------------- 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 : 0.741 6.836 15441 Z= 0.652 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 0.74078 / 0.65 (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 : 0.171 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: 0.7049 (mtt-85) 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: 0.6546 time to fit residues: 65.5134 Evaluate side-chains 84 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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: 1.9990 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: 5.9990 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 = 0.4229 r_free = 0.4229 target = 0.192010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132129 restraints weight = 11649.152| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.41 r_work: 0.3491 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10752 Z= 0.199 Angle : 0.650 7.632 15441 Z= 0.381 Chirality : 0.047 0.245 1758 Planarity : 0.005 0.054 1202 Dihedral : 30.846 169.249 3177 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.20 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 : -1.07 (0.41), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 0.00412 / 0.20 (10752) covalent geometry : angle 0.64959 / 0.38 (15441) hydrogen bonds : bond 0.05248 / 3.50 ( 680) hydrogen bonds : angle 3.23833 / 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 108 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.243 Fit side-chains REVERT: A 76 GLN cc_start: 0.8308 (tp40) cc_final: 0.8077 (tp40) REVERT: B 44 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7938 (mtmt) REVERT: B 79 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7794 (mtmt) REVERT: C 24 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: C 77 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.6961 (mtt90) REVERT: D 93 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: G 74 LYS cc_start: 0.8521 (mppt) cc_final: 0.8320 (mppt) REVERT: H 108 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7800 (tttm) outliers start: 31 outliers final: 15 residues processed: 102 average time/residue: 0.6813 time to fit residues: 72.9883 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 : 0.176 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.192695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132845 restraints weight = 11685.823| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.41 r_work: 0.3504 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0788 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= 0.170 Angle : 0.618 7.458 15441 Z= 0.364 Chirality : 0.045 0.237 1758 Planarity : 0.005 0.057 1202 Dihedral : 30.971 169.736 3171 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 1.89 (0.31), residues: 706 helix: 1.91 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.00 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 35 TYR 0.011 0.001 TYR C 57 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (10752) covalent geometry : angle 0.61772 / 0.36 (15441) hydrogen bonds : bond 0.04890 / 3.26 ( 680) hydrogen bonds : angle 3.13578 / 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 : 0.197 Fit side-chains REVERT: B 44 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7898 (mtmt) REVERT: C 24 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7068 (mp10) REVERT: C 77 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7026 (mtt-85) REVERT: D 93 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: G 71 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6648 (ttp-110) REVERT: H 108 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7691 (tttm) outliers start: 22 outliers final: 12 residues processed: 88 average time/residue: 0.7335 time to fit residues: 67.8749 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 : 0.478 ------------------------------------------------------------------------------- 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: 0.2980 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.190948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.130967 restraints weight = 11845.926| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.43 r_work: 0.3473 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1049 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= 0.190 Angle : 0.631 7.967 15441 Z= 0.367 Chirality : 0.046 0.246 1758 Planarity : 0.005 0.054 1202 Dihedral : 31.199 168.594 3168 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.08 % Allowed : 26.02 % 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: 1.86 (0.31), residues: 706 helix: 1.92 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.05 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 35 TYR 0.011 0.002 TYR C 57 PHE 0.016 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (10752) covalent geometry : angle 0.63101 / 0.37 (15441) hydrogen bonds : bond 0.05085 / 3.38 ( 680) hydrogen bonds : angle 3.10333 / 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 103 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.279 Fit side-chains REVERT: B 44 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7945 (mtmt) REVERT: B 79 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7727 (mtmt) REVERT: B 80 THR cc_start: 0.9025 (m) cc_final: 0.8770 (t) REVERT: C 24 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7063 (mp10) REVERT: C 77 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7022 (mtt-85) REVERT: D 93 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: G 92 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: H 108 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7719 (tttm) outliers start: 24 outliers final: 14 residues processed: 96 average time/residue: 0.7282 time to fit residues: 73.3343 Evaluate side-chains 95 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.191732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.131993 restraints weight = 11701.308| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.40 r_work: 0.3492 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1054 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= 0.158 Angle : 0.620 7.865 15441 Z= 0.361 Chirality : 0.045 0.244 1758 Planarity : 0.005 0.060 1202 Dihedral : 31.204 168.824 3168 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.25 % Allowed : 26.02 % Favored : 69.73 % 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: 2.07 (0.31), residues: 706 helix: 2.07 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.00 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 35 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 0.00309 / 0.16 (10752) covalent geometry : angle 0.62017 / 0.36 (15441) hydrogen bonds : bond 0.04811 / 3.20 ( 680) hydrogen bonds : angle 3.07848 / 2.22 ( 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: 25 poor density : 72 time to evaluate : 0.294 Fit side-chains REVERT: B 44 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7937 (mtmt) REVERT: B 79 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7712 (mtmt) REVERT: B 80 THR cc_start: 0.9014 (m) cc_final: 0.8771 (t) REVERT: C 24 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7058 (mp10) REVERT: C 77 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7001 (mtt-85) REVERT: D 93 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: F 84 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8367 (mmm) REVERT: G 92 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: H 108 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7680 (tttm) outliers start: 25 outliers final: 15 residues processed: 90 average time/residue: 0.6807 time to fit residues: 64.3722 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 : 0.198 ------------------------------------------------------------------------------- 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 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 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 F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 84 MET 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=3.00 ------------------------------------------------------------------------------- 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: 5.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.192151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132449 restraints weight = 11879.306| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.42 r_work: 0.3492 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1064 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= 0.149 Angle : 0.615 11.581 15441 Z= 0.357 Chirality : 0.044 0.242 1758 Planarity : 0.005 0.064 1202 Dihedral : 31.201 168.967 3168 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.91 % Allowed : 26.87 % Favored : 69.22 % 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 (0.32), residues: 706 helix: 2.17 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.94 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 35 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 0.00283 / 0.15 (10752) covalent geometry : angle 0.61466 / 0.36 (15441) hydrogen bonds : bond 0.04651 / 3.10 ( 680) hydrogen bonds : angle 3.03810 / 2.20 ( 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 97 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.211 Fit side-chains REVERT: B 44 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7936 (mtmt) REVERT: B 80 THR cc_start: 0.9002 (m) cc_final: 0.8762 (t) REVERT: C 24 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: C 77 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7009 (mtt-85) REVERT: D 93 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: H 108 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7677 (tttm) outliers start: 23 outliers final: 16 residues processed: 91 average time/residue: 0.7223 time to fit residues: 68.8947 Evaluate side-chains 92 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 C residue 102 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN F 25 ASN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.189131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129330 restraints weight = 11647.719| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.41 r_work: 0.3452 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10752 Z= 0.238 Angle : 0.671 8.328 15441 Z= 0.382 Chirality : 0.048 0.251 1758 Planarity : 0.005 0.061 1202 Dihedral : 31.318 167.067 3168 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.27 % Allowed : 25.17 % 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: 1.66 (0.31), residues: 706 helix: 1.78 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.14 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.013 0.002 TYR C 57 PHE 0.019 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 (10752) covalent geometry : angle 0.67115 / 0.38 (15441) hydrogen bonds : bond 0.05559 / 3.69 ( 680) hydrogen bonds : angle 3.18248 / 2.30 ( 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 107 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.172 Fit side-chains REVERT: B 44 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.7979 (mtmt) REVERT: B 80 THR cc_start: 0.9078 (m) cc_final: 0.8846 (t) REVERT: C 77 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7041 (mtt-85) REVERT: D 93 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.7763 (mp0) outliers start: 31 outliers final: 18 residues processed: 100 average time/residue: 0.6704 time to fit residues: 70.3062 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 : 0.160 ------------------------------------------------------------------------------- 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 102 ILE 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 94 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 87 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 105 GLU 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: 0.5980 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.191525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.132100 restraints weight = 11669.792| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.41 r_work: 0.3495 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1243 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 : 0.623 10.245 15441 Z= 0.360 Chirality : 0.046 0.247 1758 Planarity : 0.005 0.083 1202 Dihedral : 31.323 168.110 3168 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.74 % Allowed : 26.70 % 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: 2.09 (0.31), residues: 706 helix: 2.10 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.01 (0.43), residues: 168 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 0.008 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (10752) covalent geometry : angle 0.62316 / 0.36 (15441) hydrogen bonds : bond 0.04666 / 3.12 ( 680) hydrogen bonds : angle 3.04682 / 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 96 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.290 Fit side-chains REVERT: B 44 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7807 (mttp) REVERT: B 80 THR cc_start: 0.9037 (m) cc_final: 0.8817 (t) REVERT: C 24 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: C 77 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.6997 (mtt-85) REVERT: D 93 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: G 92 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: H 108 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7653 (tttm) outliers start: 22 outliers final: 16 residues processed: 90 average time/residue: 0.7269 time to fit residues: 68.8034 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 : 0.230 ------------------------------------------------------------------------------- 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 E residue 94 GLU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 79 optimal weight: 30.0000 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.191542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131624 restraints weight = 11749.488| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.41 r_work: 0.3492 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10752 Z= 0.151 Angle : 0.622 13.521 15441 Z= 0.358 Chirality : 0.044 0.247 1758 Planarity : 0.005 0.061 1202 Dihedral : 31.299 168.128 3168 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.40 % Allowed : 27.21 % Favored : 69.39 % 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 (0.31), residues: 706 helix: 2.18 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.99 (0.43), residues: 170 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 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (10752) covalent geometry : angle 0.62177 / 0.36 (15441) hydrogen bonds : bond 0.04638 / 3.10 ( 680) hydrogen bonds : angle 3.05423 / 2.21 ( 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: 20 poor density : 73 time to evaluate : 0.262 Fit side-chains REVERT: A 133 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: B 44 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7806 (mttp) REVERT: B 80 THR cc_start: 0.9020 (m) cc_final: 0.8793 (t) REVERT: C 24 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: C 77 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.6920 (mtt-85) REVERT: D 93 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: H 108 LYS cc_start: 0.7790 (mtpp) cc_final: 0.7590 (tttm) outliers start: 20 outliers final: 13 residues processed: 90 average time/residue: 0.7251 time to fit residues: 68.4759 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 : 0.188 ------------------------------------------------------------------------------- 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 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 H residue 39 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 105 GLU 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: 1.9990 chunk 80 optimal weight: 50.0000 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 30.0000 chunk 89 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 68 optimal weight: 0.0010 chunk 23 optimal weight: 0.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.191928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132085 restraints weight = 11639.695| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.42 r_work: 0.3495 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10752 Z= 0.146 Angle : 0.625 18.130 15441 Z= 0.358 Chirality : 0.044 0.248 1758 Planarity : 0.005 0.068 1202 Dihedral : 31.290 168.397 3166 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.89 % Allowed : 27.72 % Favored : 69.39 % 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: 2.22 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.97 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 35 TYR 0.009 0.001 TYR C 57 PHE 0.010 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (10752) covalent geometry : angle 0.62484 / 0.36 (15441) hydrogen bonds : bond 0.04553 / 3.04 ( 680) hydrogen bonds : angle 3.02902 / 2.19 ( 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 89 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.171 Fit side-chains REVERT: A 133 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: B 44 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7809 (mttp) REVERT: B 49 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8215 (mt) REVERT: B 80 THR cc_start: 0.9015 (m) cc_final: 0.8787 (t) REVERT: C 24 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: C 77 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.6928 (mtt-85) REVERT: D 93 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: G 71 ARG cc_start: 0.7472 (ttp-110) cc_final: 0.7272 (ttp-110) REVERT: H 108 LYS cc_start: 0.7779 (mtpp) cc_final: 0.7576 (tttm) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 0.7537 time to fit residues: 67.9276 Evaluate side-chains 86 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 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 H residue 39 VAL Chi-restraints excluded: chain H residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.0570 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 17 optimal weight: 7.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.192218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132305 restraints weight = 11817.088| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.42 r_work: 0.3500 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10752 Z= 0.140 Angle : 0.624 20.125 15441 Z= 0.356 Chirality : 0.044 0.248 1758 Planarity : 0.005 0.084 1202 Dihedral : 31.288 168.509 3165 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.55 % Allowed : 28.23 % Favored : 69.22 % 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: 2.33 (0.32), residues: 706 helix: 2.30 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -0.96 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 35 TYR 0.009 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 0.00256 / 0.14 (10752) covalent geometry : angle 0.62365 / 0.36 (15441) hydrogen bonds : bond 0.04484 / 3.00 ( 680) hydrogen bonds : angle 3.01780 / 2.18 ( 1742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2900.02 seconds wall clock time: 49 minutes 53.36 seconds (2993.36 seconds total)