Starting phenix.real_space_refine on Thu Aug 6 09:17:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9si9_54926/08_2026/9si9_54926.cif Found real_map, /net/cci-nas-00/data/ceres_data/9si9_54926/08_2026/9si9_54926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9si9_54926/08_2026/9si9_54926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9si9_54926/08_2026/9si9_54926.map" model { file = "/net/cci-nas-00/data/ceres_data/9si9_54926/08_2026/9si9_54926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9si9_54926/08_2026/9si9_54926.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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 294 5.49 5 S 26 5.16 5 C 8184 2.51 5 N 2701 2.21 5 O 3266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 14471 Number of models: 1 Model: "" Number of chains: 14 Chain: "I" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3034 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2990 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 871 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "L" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 633 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "M" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "N" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 380 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "E" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 108 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Time building chain proxies: 3.01, per 1000 atoms: 0.21 Number of scatterers: 14471 At special positions: 0 Unit cell: (96.691, 149.762, 119.228, 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 26 16.00 P 294 15.00 O 3266 8.00 N 2701 7.00 C 8184 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: 1.14 Conformation dependent library (CDL) restraints added in 477.3 milliseconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 71.0% alpha, 1.5% beta 147 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.512A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.811A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.522A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) 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 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 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 removed outlier: 3.534A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.950A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.691A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.539A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.537A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.177A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 61 removed outlier: 3.552A pdb=" N ILE L 58 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU L 59 " --> pdb=" O ASN L 55 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 68 Processing helix chain 'L' and resid 69 through 75 Processing helix chain 'M' and resid 7 through 11 removed outlier: 3.869A pdb=" N GLN M 11 " --> pdb=" O PRO M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.781A pdb=" N ARG M 18 " --> pdb=" O LEU M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 42 removed outlier: 4.219A pdb=" N MET M 38 " --> pdb=" O THR M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 81 Processing helix chain 'M' and resid 92 through 96 removed outlier: 3.555A pdb=" N LEU M 96 " --> pdb=" O PHE M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 141 removed outlier: 4.195A pdb=" N MET M 141 " --> pdb=" O GLN M 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 45 removed outlier: 4.111A pdb=" N LEU N 11 " --> pdb=" O GLY N 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.038A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.610A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 17 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.184A 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 'C' and resid 42 through 43 removed outlier: 7.430A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.559A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.488A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 548 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 754 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3066 1.33 - 1.45: 4506 1.45 - 1.57: 7125 1.57 - 1.69: 585 1.69 - 1.81: 43 Bond restraints: 15325 Sorted by residual: bond pdb=" C3' DT J 161 " pdb=" C2' DT J 161 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3' DC I 48 " pdb=" O3' DC I 48 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.73e+00 bond pdb=" C3' DC J 239 " pdb=" C2' DC J 239 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.56e+00 bond pdb=" C1' DT I 49 " pdb=" N1 DT I 49 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.38e+00 bond pdb=" C3' DC J 199 " pdb=" C2' DC J 199 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.32e+00 ... (remaining 15320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 21331 2.19 - 4.38: 559 4.38 - 6.58: 18 6.58 - 8.77: 12 8.77 - 10.96: 4 Bond angle restraints: 21924 Sorted by residual: angle pdb=" O4' DC J 289 " pdb=" C4' DC J 289 " pdb=" C3' DC J 289 " ideal model delta sigma weight residual 106.00 102.87 3.13 6.00e-01 2.78e+00 2.73e+01 angle pdb=" O4' DG J 171 " pdb=" C4' DG J 171 " pdb=" C3' DG J 171 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.22e+01 angle pdb=" N3 DT J 178 " pdb=" C4 DT J 178 " pdb=" O4 DT J 178 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" O4' DT I 139 " pdb=" C4' DT I 139 " pdb=" C3' DT I 139 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" O4' DT I 118 " pdb=" C4' DT I 118 " pdb=" C3' DT I 118 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 21919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.27: 5935 20.27 - 40.53: 1378 40.53 - 60.80: 1143 60.80 - 81.07: 61 81.07 - 101.33: 16 Dihedral angle restraints: 8533 sinusoidal: 5469 harmonic: 3064 Sorted by residual: dihedral pdb=" CA LEU G 116 " pdb=" C LEU G 116 " pdb=" N PRO G 117 " pdb=" CA PRO G 117 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CG ARG G 77 " pdb=" CD ARG G 77 " pdb=" NE ARG G 77 " pdb=" CZ ARG G 77 " ideal model delta sinusoidal sigma weight residual -90.00 -40.26 -49.74 2 1.50e+01 4.44e-03 1.24e+01 dihedral pdb=" CG ARG E 53 " pdb=" CD ARG E 53 " pdb=" NE ARG E 53 " pdb=" CZ ARG E 53 " ideal model delta sinusoidal sigma weight residual 90.00 41.01 48.99 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 8530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1956 0.054 - 0.108: 449 0.108 - 0.162: 63 0.162 - 0.217: 2 0.217 - 0.271: 2 Chirality restraints: 2472 Sorted by residual: chirality pdb=" CG LEU N 34 " pdb=" CB LEU N 34 " pdb=" CD1 LEU N 34 " pdb=" CD2 LEU N 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU C 63 " pdb=" CB LEU C 63 " pdb=" CD1 LEU C 63 " pdb=" CD2 LEU C 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASN C 38 " pdb=" N ASN C 38 " pdb=" C ASN C 38 " pdb=" CB ASN C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2469 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP N 30 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" CG ASP N 30 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP N 30 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP N 30 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 60 " -0.021 2.00e-02 2.50e+03 9.61e-03 2.54e+00 pdb=" N9 DA I 60 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 60 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 60 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 60 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 60 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 60 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 60 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 60 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 60 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 60 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO C 80 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.022 5.00e-02 4.00e+02 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 6433 2.98 - 3.46: 14416 3.46 - 3.94: 28098 3.94 - 4.42: 31437 4.42 - 4.90: 42626 Nonbonded interactions: 123010 Sorted by model distance: nonbonded pdb=" O ASN C 38 " pdb=" OD1 ASN C 38 " model vdw 2.502 3.040 nonbonded pdb=" O MET N 26 " pdb=" OD1 ASP N 30 " model vdw 2.533 3.040 nonbonded pdb=" O ASN C 110 " pdb=" OD1 ASN C 110 " model vdw 2.573 3.040 nonbonded pdb=" O ASP N 27 " pdb=" OD1 ASP N 30 " model vdw 2.578 3.040 nonbonded pdb=" O4' DC J 241 " pdb=" C6 DC J 241 " model vdw 2.584 2.672 ... (remaining 123005 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 37 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 9 through 120) } ncs_group { reference = chain 'D' 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=0.00 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: 4.380 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: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.770 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15325 Z= 0.526 Angle : 0.768 10.960 21924 Z= 0.652 Chirality : 0.046 0.271 2472 Planarity : 0.004 0.039 1762 Dihedral : 27.269 101.335 6541 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.01 % Allowed : 13.23 % Favored : 85.76 % 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: 1.92 (0.26), residues: 1025 helix: 2.20 (0.19), residues: 703 sheet: None (None), residues: 0 loop : -0.87 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 77 TYR 0.010 0.001 TYR F 51 PHE 0.020 0.002 PHE C 25 TRP 0.007 0.001 TRP M 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.53 (15325) covalent geometry : angle 0.76765 / 0.65 (21924) hydrogen bonds : bond 0.09820 / 10.65 ( 925) hydrogen bonds : angle 3.77828 / 5.28 ( 2359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 308 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8556 (mtm) REVERT: L 17 ARG cc_start: 0.8719 (mtp180) cc_final: 0.8478 (mtp180) REVERT: L 31 GLU cc_start: 0.8991 (tp30) cc_final: 0.8664 (tm-30) REVERT: L 68 MET cc_start: 0.3361 (pp-130) cc_final: 0.3112 (pp-130) REVERT: M 65 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6743 (mp0) REVERT: M 92 GLN cc_start: 0.8132 (mp10) cc_final: 0.7844 (mp10) REVERT: M 100 GLU cc_start: 0.7262 (tp30) cc_final: 0.5572 (mt-10) REVERT: M 120 LYS cc_start: 0.9026 (tppt) cc_final: 0.8803 (mmmt) REVERT: M 127 THR cc_start: 0.9306 (m) cc_final: 0.8170 (p) REVERT: M 130 LYS cc_start: 0.9489 (ptmt) cc_final: 0.8937 (pttp) REVERT: N 42 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8305 (mm-30) REVERT: N 44 MET cc_start: 0.8673 (tmm) cc_final: 0.7259 (tmm) outliers start: 9 outliers final: 4 residues processed: 313 average time/residue: 0.8096 time to fit residues: 271.1786 Evaluate side-chains 246 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 241 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 27 GLN B 93 GLN G 73 ASN G 89 ASN L 14 ASN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 93 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.086051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.054101 restraints weight = 41535.697| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.58 r_work: 0.2708 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15325 Z= 0.162 Angle : 0.679 9.973 21924 Z= 0.389 Chirality : 0.044 0.222 2472 Planarity : 0.005 0.045 1762 Dihedral : 30.183 151.652 4381 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.04 % Allowed : 19.96 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.26), residues: 1025 helix: 2.30 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.81 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 132 TYR 0.011 0.001 TYR B 51 PHE 0.024 0.002 PHE N 22 TRP 0.020 0.002 TRP N 33 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (15325) covalent geometry : angle 0.67910 / 0.39 (21924) hydrogen bonds : bond 0.04564 / 5.06 ( 925) hydrogen bonds : angle 3.35940 / 4.86 ( 2359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7235 (t70) cc_final: 0.6764 (t70) REVERT: A 59 GLU cc_start: 0.8656 (pm20) cc_final: 0.8274 (pm20) REVERT: B 59 LYS cc_start: 0.9425 (ttpp) cc_final: 0.9208 (ttpp) REVERT: F 59 LYS cc_start: 0.9395 (tppp) cc_final: 0.9194 (tptp) REVERT: G 19 SER cc_start: 0.9621 (OUTLIER) cc_final: 0.9375 (p) REVERT: H 63 ASN cc_start: 0.8907 (t0) cc_final: 0.8628 (m-40) REVERT: L 26 LYS cc_start: 0.9139 (ttpp) cc_final: 0.8854 (pptt) REVERT: L 29 ASP cc_start: 0.9661 (m-30) cc_final: 0.9230 (p0) REVERT: L 31 GLU cc_start: 0.9221 (tp30) cc_final: 0.8921 (tm-30) REVERT: L 35 ARG cc_start: 0.9205 (mmt180) cc_final: 0.8779 (mmt90) REVERT: L 68 MET cc_start: 0.6204 (pp-130) cc_final: 0.5862 (pp-130) REVERT: M 96 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6493 (mm) REVERT: M 127 THR cc_start: 0.9294 (m) cc_final: 0.9008 (p) REVERT: M 130 LYS cc_start: 0.9558 (ptmt) cc_final: 0.9201 (pttp) REVERT: N 42 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8644 (mm-30) outliers start: 45 outliers final: 14 residues processed: 269 average time/residue: 0.8210 time to fit residues: 236.3531 Evaluate side-chains 251 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 40 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 93 GLN C 94 ASN G 24 GLN G 89 ASN H 47 GLN ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.085143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.053003 restraints weight = 41797.369| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.56 r_work: 0.2686 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15325 Z= 0.185 Angle : 0.662 8.006 21924 Z= 0.377 Chirality : 0.043 0.279 2472 Planarity : 0.005 0.039 1762 Dihedral : 30.291 103.569 4373 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.70 % Allowed : 22.31 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.26), residues: 1025 helix: 2.42 (0.19), residues: 711 sheet: None (None), residues: 0 loop : -0.84 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 86 TYR 0.012 0.001 TYR D 42 PHE 0.018 0.002 PHE M 22 TRP 0.008 0.001 TRP M 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (15325) covalent geometry : angle 0.66199 / 0.38 (21924) hydrogen bonds : bond 0.04516 / 4.97 ( 925) hydrogen bonds : angle 3.21368 / 4.70 ( 2359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7416 (t70) cc_final: 0.7030 (t70) REVERT: A 59 GLU cc_start: 0.8708 (pm20) cc_final: 0.8332 (pm20) REVERT: B 59 LYS cc_start: 0.9433 (ttpp) cc_final: 0.9216 (ttpp) REVERT: G 19 SER cc_start: 0.9608 (OUTLIER) cc_final: 0.9393 (p) REVERT: H 63 ASN cc_start: 0.8966 (t0) cc_final: 0.8727 (m-40) REVERT: L 14 ASN cc_start: 0.9651 (m-40) cc_final: 0.9385 (m110) REVERT: L 25 LEU cc_start: 0.9480 (mm) cc_final: 0.9266 (tm) REVERT: L 26 LYS cc_start: 0.9309 (ttpp) cc_final: 0.9045 (pptt) REVERT: L 29 ASP cc_start: 0.9663 (m-30) cc_final: 0.9144 (p0) REVERT: L 30 ARG cc_start: 0.9475 (ttm110) cc_final: 0.9227 (ttm-80) REVERT: L 31 GLU cc_start: 0.9261 (tp30) cc_final: 0.8917 (tm-30) REVERT: L 68 MET cc_start: 0.6162 (pp-130) cc_final: 0.5750 (pp-130) REVERT: M 130 LYS cc_start: 0.9583 (ptmt) cc_final: 0.9259 (pptt) REVERT: M 133 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8655 (tmm160) REVERT: N 19 LEU cc_start: 0.8824 (tm) cc_final: 0.8497 (tt) REVERT: N 42 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8800 (mm-30) outliers start: 33 outliers final: 17 residues processed: 261 average time/residue: 0.6882 time to fit residues: 192.7688 Evaluate side-chains 252 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 122 optimal weight: 0.2980 chunk 17 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 93 GLN C 94 ASN D 63 ASN G 89 ASN L 44 GLN ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN E 76 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.084960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.052921 restraints weight = 41762.267| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.53 r_work: 0.2662 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15325 Z= 0.182 Angle : 0.653 8.348 21924 Z= 0.369 Chirality : 0.043 0.245 2472 Planarity : 0.004 0.045 1762 Dihedral : 30.375 105.040 4373 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.71 % Allowed : 21.64 % Favored : 73.65 % 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: 2.23 (0.26), residues: 1025 helix: 2.43 (0.18), residues: 712 sheet: None (None), residues: 0 loop : -0.83 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 43 TYR 0.010 0.001 TYR F 51 PHE 0.016 0.002 PHE M 22 TRP 0.007 0.001 TRP M 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 (15325) covalent geometry : angle 0.65344 / 0.37 (21924) hydrogen bonds : bond 0.04318 / 4.74 ( 925) hydrogen bonds : angle 3.19240 / 4.67 ( 2359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7493 (t70) cc_final: 0.7142 (t70) REVERT: A 59 GLU cc_start: 0.8694 (pm20) cc_final: 0.8316 (pm20) REVERT: G 19 SER cc_start: 0.9602 (OUTLIER) cc_final: 0.9393 (p) REVERT: G 92 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8034 (mt-10) REVERT: H 63 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8753 (m-40) REVERT: L 14 ASN cc_start: 0.9642 (m-40) cc_final: 0.9374 (m110) REVERT: L 20 LYS cc_start: 0.8774 (pptt) cc_final: 0.8074 (pptt) REVERT: L 26 LYS cc_start: 0.9335 (ttpp) cc_final: 0.9031 (pptt) REVERT: L 31 GLU cc_start: 0.9289 (tp30) cc_final: 0.8902 (tm-30) REVERT: L 68 MET cc_start: 0.6142 (pp-130) cc_final: 0.5761 (pp-130) REVERT: M 40 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7870 (pp20) REVERT: M 130 LYS cc_start: 0.9577 (ptmt) cc_final: 0.9269 (pptt) REVERT: M 133 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8705 (tmm160) REVERT: N 20 MET cc_start: 0.8988 (mpp) cc_final: 0.8562 (ppp) REVERT: N 33 TRP cc_start: 0.7701 (t-100) cc_final: 0.7456 (t-100) REVERT: N 44 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8044 (tmm) outliers start: 42 outliers final: 22 residues processed: 252 average time/residue: 0.6938 time to fit residues: 187.3436 Evaluate side-chains 257 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain N residue 44 MET Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 113 optimal weight: 40.0000 chunk 123 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 73 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 93 GLN C 94 ASN D 63 ASN G 24 GLN G 89 ASN L 44 GLN ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.085800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.053971 restraints weight = 41468.236| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.54 r_work: 0.2712 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15325 Z= 0.139 Angle : 0.632 8.421 21924 Z= 0.360 Chirality : 0.041 0.196 2472 Planarity : 0.005 0.058 1762 Dihedral : 30.333 106.286 4373 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.82 % Allowed : 21.30 % Favored : 73.88 % 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: 2.33 (0.26), residues: 1025 helix: 2.49 (0.19), residues: 713 sheet: None (None), residues: 0 loop : -0.76 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 43 TYR 0.011 0.001 TYR D 40 PHE 0.015 0.001 PHE M 22 TRP 0.006 0.001 TRP M 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (15325) covalent geometry : angle 0.63214 / 0.36 (21924) hydrogen bonds : bond 0.03992 / 4.43 ( 925) hydrogen bonds : angle 3.08116 / 4.49 ( 2359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7502 (t70) cc_final: 0.7171 (t70) REVERT: A 59 GLU cc_start: 0.8678 (pm20) cc_final: 0.8315 (pm20) REVERT: B 92 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8401 (ttp80) REVERT: C 95 LYS cc_start: 0.9439 (ttmm) cc_final: 0.9147 (tppt) REVERT: D 43 LYS cc_start: 0.9514 (mttm) cc_final: 0.9272 (mttp) REVERT: F 92 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8612 (ttp80) REVERT: G 92 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8006 (mt-10) REVERT: H 63 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8731 (m-40) REVERT: L 14 ASN cc_start: 0.9654 (m-40) cc_final: 0.9422 (m110) REVERT: L 15 SER cc_start: 0.9709 (OUTLIER) cc_final: 0.9421 (p) REVERT: L 26 LYS cc_start: 0.9361 (ttpp) cc_final: 0.9067 (pptt) REVERT: L 29 ASP cc_start: 0.9595 (m-30) cc_final: 0.9082 (p0) REVERT: L 30 ARG cc_start: 0.9416 (ttm110) cc_final: 0.9172 (ttm-80) REVERT: L 31 GLU cc_start: 0.9302 (tp30) cc_final: 0.8979 (tm-30) REVERT: L 35 ARG cc_start: 0.9163 (mmt180) cc_final: 0.8612 (ttt180) REVERT: L 68 MET cc_start: 0.6147 (pp-130) cc_final: 0.5751 (pp-130) REVERT: M 40 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7814 (pp20) REVERT: M 96 LEU cc_start: 0.6693 (mm) cc_final: 0.6458 (mm) REVERT: M 130 LYS cc_start: 0.9562 (ptmt) cc_final: 0.9289 (pptt) REVERT: M 133 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8674 (tmm160) REVERT: N 33 TRP cc_start: 0.7681 (t-100) cc_final: 0.7409 (t-100) REVERT: N 42 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8408 (mm-30) outliers start: 43 outliers final: 19 residues processed: 269 average time/residue: 0.7398 time to fit residues: 213.5461 Evaluate side-chains 264 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN B 93 GLN G 24 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.084665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.052875 restraints weight = 41663.824| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.51 r_work: 0.2679 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15325 Z= 0.197 Angle : 0.668 10.115 21924 Z= 0.373 Chirality : 0.043 0.304 2472 Planarity : 0.005 0.050 1762 Dihedral : 30.448 107.890 4373 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.48 % Allowed : 21.97 % Favored : 73.54 % 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 (0.26), residues: 1025 helix: 2.40 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -0.77 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 43 TYR 0.014 0.001 TYR D 40 PHE 0.014 0.002 PHE C 25 TRP 0.005 0.001 TRP M 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.20 (15325) covalent geometry : angle 0.66807 / 0.37 (21924) hydrogen bonds : bond 0.04496 / 4.92 ( 925) hydrogen bonds : angle 3.16023 / 4.60 ( 2359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7528 (t70) cc_final: 0.7154 (t70) REVERT: A 59 GLU cc_start: 0.8668 (pm20) cc_final: 0.8295 (pm20) REVERT: B 59 LYS cc_start: 0.9436 (ttmm) cc_final: 0.9167 (ttpp) REVERT: B 63 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8964 (mt-10) REVERT: B 74 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8608 (mm-30) REVERT: B 92 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8425 (ttp80) REVERT: C 64 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.9143 (tt0) REVERT: C 95 LYS cc_start: 0.9431 (ttmm) cc_final: 0.9158 (tppt) REVERT: G 92 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8076 (mt-10) REVERT: H 63 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8756 (m-40) REVERT: L 14 ASN cc_start: 0.9663 (m-40) cc_final: 0.9428 (m110) REVERT: L 15 SER cc_start: 0.9703 (OUTLIER) cc_final: 0.9419 (p) REVERT: L 20 LYS cc_start: 0.8892 (pptt) cc_final: 0.8540 (pptt) REVERT: L 26 LYS cc_start: 0.9382 (ttpp) cc_final: 0.9069 (pptt) REVERT: L 29 ASP cc_start: 0.9559 (m-30) cc_final: 0.8978 (p0) REVERT: L 30 ARG cc_start: 0.9434 (ttm110) cc_final: 0.9180 (ttm-80) REVERT: L 31 GLU cc_start: 0.9335 (tp30) cc_final: 0.9015 (tm-30) REVERT: L 35 ARG cc_start: 0.9153 (mmt180) cc_final: 0.8634 (ttt180) REVERT: L 68 MET cc_start: 0.6223 (pp-130) cc_final: 0.5796 (pp-130) REVERT: M 40 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7880 (pp20) REVERT: M 116 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8289 (pp20) REVERT: M 130 LYS cc_start: 0.9586 (ptmt) cc_final: 0.9373 (pptt) REVERT: M 133 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8702 (tmm160) REVERT: N 20 MET cc_start: 0.9027 (mpp) cc_final: 0.8677 (ppp) REVERT: N 33 TRP cc_start: 0.7693 (t-100) cc_final: 0.7485 (t-100) REVERT: N 44 MET cc_start: 0.8564 (tmm) cc_final: 0.7984 (tmm) outliers start: 40 outliers final: 23 residues processed: 253 average time/residue: 0.6996 time to fit residues: 189.1365 Evaluate side-chains 257 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain O residue 8 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN B 93 GLN C 94 ASN G 24 GLN ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.085100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.053109 restraints weight = 41482.332| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.50 r_work: 0.2665 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15325 Z= 0.168 Angle : 0.655 9.116 21924 Z= 0.367 Chirality : 0.042 0.326 2472 Planarity : 0.004 0.048 1762 Dihedral : 30.463 109.417 4373 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.26 % Allowed : 22.65 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.26), residues: 1025 helix: 2.38 (0.19), residues: 717 sheet: None (None), residues: 0 loop : -0.71 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 43 TYR 0.015 0.001 TYR D 40 PHE 0.013 0.001 PHE M 22 TRP 0.007 0.001 TRP M 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (15325) covalent geometry : angle 0.65489 / 0.37 (21924) hydrogen bonds : bond 0.04110 / 4.54 ( 925) hydrogen bonds : angle 3.11747 / 4.52 ( 2359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7576 (t70) cc_final: 0.7268 (t70) REVERT: A 59 GLU cc_start: 0.8664 (pm20) cc_final: 0.8302 (pm20) REVERT: B 59 LYS cc_start: 0.9443 (ttmm) cc_final: 0.9185 (ttpp) REVERT: B 63 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8989 (mt-10) REVERT: B 92 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8447 (ttp80) REVERT: C 64 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.9150 (tt0) REVERT: C 95 LYS cc_start: 0.9422 (ttmm) cc_final: 0.9159 (tppt) REVERT: G 92 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8245 (mt-10) REVERT: H 63 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8766 (m-40) REVERT: H 106 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9196 (mp) REVERT: L 14 ASN cc_start: 0.9654 (m-40) cc_final: 0.9422 (m110) REVERT: L 15 SER cc_start: 0.9709 (OUTLIER) cc_final: 0.9477 (p) REVERT: L 26 LYS cc_start: 0.9392 (ttpp) cc_final: 0.9095 (pptt) REVERT: L 28 PHE cc_start: 0.9520 (t80) cc_final: 0.9216 (t80) REVERT: L 29 ASP cc_start: 0.9563 (m-30) cc_final: 0.9100 (p0) REVERT: L 31 GLU cc_start: 0.9341 (tp30) cc_final: 0.9024 (tm-30) REVERT: L 35 ARG cc_start: 0.9141 (mmt180) cc_final: 0.8638 (ttt180) REVERT: L 68 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5826 (pp-130) REVERT: M 40 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7800 (pp20) REVERT: M 116 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8317 (pp20) REVERT: M 130 LYS cc_start: 0.9577 (ptmt) cc_final: 0.9330 (pptt) REVERT: M 133 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8683 (tmm160) REVERT: N 20 MET cc_start: 0.9062 (mpp) cc_final: 0.8650 (ppp) REVERT: N 42 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8623 (mm-30) outliers start: 38 outliers final: 19 residues processed: 250 average time/residue: 0.7857 time to fit residues: 210.2987 Evaluate side-chains 256 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain O residue 8 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 100 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN D 63 ASN ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.084752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.052688 restraints weight = 41357.903| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.52 r_work: 0.2683 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15325 Z= 0.180 Angle : 0.669 9.978 21924 Z= 0.371 Chirality : 0.042 0.335 2472 Planarity : 0.005 0.063 1762 Dihedral : 30.482 110.663 4373 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.04 % Allowed : 23.09 % Favored : 72.87 % 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 (0.26), residues: 1025 helix: 2.34 (0.19), residues: 717 sheet: None (None), residues: 0 loop : -0.73 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 43 TYR 0.016 0.001 TYR D 40 PHE 0.012 0.001 PHE M 22 TRP 0.017 0.002 TRP N 33 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 (15325) covalent geometry : angle 0.66905 / 0.37 (21924) hydrogen bonds : bond 0.04218 / 4.65 ( 925) hydrogen bonds : angle 3.12813 / 4.51 ( 2359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7585 (t70) cc_final: 0.7227 (t70) REVERT: A 59 GLU cc_start: 0.8653 (pm20) cc_final: 0.8284 (pm20) REVERT: B 59 LYS cc_start: 0.9448 (ttmm) cc_final: 0.9224 (ttpp) REVERT: B 92 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8471 (ttp80) REVERT: C 64 GLU cc_start: 0.9438 (OUTLIER) cc_final: 0.9157 (tt0) REVERT: C 95 LYS cc_start: 0.9414 (ttmm) cc_final: 0.9153 (tppt) REVERT: G 92 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8311 (mt-10) REVERT: H 63 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8768 (m-40) REVERT: H 101 LEU cc_start: 0.9633 (mm) cc_final: 0.9399 (mm) REVERT: L 14 ASN cc_start: 0.9646 (m-40) cc_final: 0.9381 (m110) REVERT: L 15 SER cc_start: 0.9704 (OUTLIER) cc_final: 0.9432 (p) REVERT: L 20 LYS cc_start: 0.8752 (pptt) cc_final: 0.8349 (pptt) REVERT: L 26 LYS cc_start: 0.9403 (ttpp) cc_final: 0.9076 (pptt) REVERT: L 28 PHE cc_start: 0.9514 (t80) cc_final: 0.9222 (t80) REVERT: L 29 ASP cc_start: 0.9524 (m-30) cc_final: 0.9058 (p0) REVERT: L 30 ARG cc_start: 0.9418 (ttm110) cc_final: 0.9166 (ttm-80) REVERT: L 31 GLU cc_start: 0.9371 (tp30) cc_final: 0.9129 (tm-30) REVERT: L 35 ARG cc_start: 0.9159 (mmt180) cc_final: 0.8659 (ttt180) REVERT: L 68 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.5856 (pp-130) REVERT: M 40 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7822 (pp20) REVERT: M 116 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8337 (pp20) REVERT: M 130 LYS cc_start: 0.9590 (ptmt) cc_final: 0.9361 (pptt) REVERT: M 133 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8682 (tmm160) REVERT: N 42 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8513 (mm-30) outliers start: 36 outliers final: 20 residues processed: 249 average time/residue: 0.7193 time to fit residues: 191.9000 Evaluate side-chains 257 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain O residue 8 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9990 chunk 119 optimal weight: 0.0870 chunk 127 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 81 optimal weight: 0.4980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 94 ASN ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.085663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053806 restraints weight = 41549.112| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.53 r_work: 0.2712 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15325 Z= 0.142 Angle : 0.669 9.794 21924 Z= 0.374 Chirality : 0.041 0.277 2472 Planarity : 0.005 0.050 1762 Dihedral : 30.394 112.043 4373 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.70 % Allowed : 24.22 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.26), residues: 1025 helix: 2.34 (0.19), residues: 717 sheet: -0.46 (2.20), residues: 10 loop : -0.67 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 43 TYR 0.017 0.001 TYR D 40 PHE 0.013 0.001 PHE M 22 TRP 0.016 0.002 TRP N 33 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (15325) covalent geometry : angle 0.66885 / 0.37 (21924) hydrogen bonds : bond 0.03930 / 4.40 ( 925) hydrogen bonds : angle 3.12026 / 4.46 ( 2359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7519 (t70) cc_final: 0.7193 (t70) REVERT: A 59 GLU cc_start: 0.8657 (pm20) cc_final: 0.8268 (pm20) REVERT: B 59 LYS cc_start: 0.9419 (ttmm) cc_final: 0.9136 (ttpp) REVERT: B 63 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8958 (mt-10) REVERT: B 92 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8468 (ttp80) REVERT: C 95 LYS cc_start: 0.9406 (ttmm) cc_final: 0.9148 (tppt) REVERT: D 116 LYS cc_start: 0.9501 (ttmm) cc_final: 0.9281 (ttmt) REVERT: H 63 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8755 (m-40) REVERT: H 101 LEU cc_start: 0.9612 (mm) cc_final: 0.9358 (mm) REVERT: L 14 ASN cc_start: 0.9631 (m-40) cc_final: 0.9391 (m110) REVERT: L 15 SER cc_start: 0.9676 (OUTLIER) cc_final: 0.9469 (p) REVERT: L 26 LYS cc_start: 0.9422 (ttpp) cc_final: 0.9123 (pptt) REVERT: L 29 ASP cc_start: 0.9504 (m-30) cc_final: 0.8973 (p0) REVERT: L 31 GLU cc_start: 0.9416 (tp30) cc_final: 0.9119 (tm-30) REVERT: L 35 ARG cc_start: 0.9127 (mmt180) cc_final: 0.8500 (mmt180) REVERT: L 68 MET cc_start: 0.6301 (OUTLIER) cc_final: 0.5866 (pp-130) REVERT: M 40 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7812 (pp20) REVERT: M 116 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8337 (pp20) REVERT: M 126 GLU cc_start: 0.9282 (tm-30) cc_final: 0.8843 (pp20) REVERT: M 133 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8702 (tmm160) REVERT: N 42 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8610 (mm-30) outliers start: 33 outliers final: 14 residues processed: 261 average time/residue: 0.7821 time to fit residues: 218.4132 Evaluate side-chains 258 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain O residue 8 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 73 ASN ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.086017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.054111 restraints weight = 41506.689| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.51 r_work: 0.2719 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15325 Z= 0.153 Angle : 0.716 13.812 21924 Z= 0.395 Chirality : 0.042 0.272 2472 Planarity : 0.005 0.064 1762 Dihedral : 30.374 112.961 4373 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.80 % Allowed : 26.01 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.26), residues: 1025 helix: 2.20 (0.19), residues: 716 sheet: -0.49 (2.21), residues: 10 loop : -0.67 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG N 43 TYR 0.070 0.002 TYR L 54 PHE 0.013 0.001 PHE M 22 TRP 0.016 0.002 TRP N 33 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (15325) covalent geometry : angle 0.71634 / 0.39 (21924) hydrogen bonds : bond 0.04096 / 4.61 ( 925) hydrogen bonds : angle 3.21793 / 4.51 ( 2359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7544 (t70) cc_final: 0.7211 (t70) REVERT: A 59 GLU cc_start: 0.8663 (pm20) cc_final: 0.8285 (pm20) REVERT: B 92 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8476 (ttp80) REVERT: C 73 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8572 (t0) REVERT: C 95 LYS cc_start: 0.9387 (ttmm) cc_final: 0.9150 (tppt) REVERT: D 116 LYS cc_start: 0.9485 (ttmm) cc_final: 0.9263 (ttmt) REVERT: G 92 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8460 (mt-10) REVERT: H 35 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8319 (mt-10) REVERT: H 63 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8777 (m-40) REVERT: H 101 LEU cc_start: 0.9620 (mm) cc_final: 0.9386 (mm) REVERT: L 26 LYS cc_start: 0.9435 (ttpp) cc_final: 0.9122 (pptt) REVERT: L 29 ASP cc_start: 0.9497 (m-30) cc_final: 0.8965 (p0) REVERT: L 31 GLU cc_start: 0.9441 (tp30) cc_final: 0.9182 (tm-30) REVERT: L 68 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.5900 (pp-130) REVERT: M 40 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7799 (pp20) REVERT: M 116 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8325 (pp20) REVERT: M 133 ARG cc_start: 0.9094 (ppt170) cc_final: 0.8725 (tmm160) outliers start: 25 outliers final: 15 residues processed: 252 average time/residue: 0.8152 time to fit residues: 219.7972 Evaluate side-chains 252 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain O residue 8 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 114 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 73 ASN C 94 ASN ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.086017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.054095 restraints weight = 41425.625| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.52 r_work: 0.2701 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 15325 Z= 0.216 Angle : 0.898 59.191 21924 Z= 0.525 Chirality : 0.042 0.258 2472 Planarity : 0.006 0.106 1762 Dihedral : 30.373 112.967 4373 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.47 % Allowed : 27.24 % Favored : 70.29 % Cbeta Deviations : 0.10 % 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: 2.04 (0.26), residues: 1025 helix: 2.19 (0.19), residues: 716 sheet: -0.49 (2.21), residues: 10 loop : -0.67 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 43 TYR 0.061 0.002 TYR L 54 PHE 0.011 0.001 PHE M 22 TRP 0.011 0.001 TRP N 33 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.22 (15325) covalent geometry : angle 0.89840 / 0.53 (21924) hydrogen bonds : bond 0.04108 / 4.63 ( 925) hydrogen bonds : angle 3.23886 / 4.52 ( 2359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5734.82 seconds wall clock time: 98 minutes 4.91 seconds (5884.91 seconds total)