Starting phenix.real_space_refine on Thu Aug 6 09:28:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmt_48403/08_2026/9mmt_48403.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmt_48403/08_2026/9mmt_48403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mmt_48403/08_2026/9mmt_48403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmt_48403/08_2026/9mmt_48403.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mmt_48403/08_2026/9mmt_48403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmt_48403/08_2026/9mmt_48403.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 178 5.49 5 S 14 5.16 5 C 4437 2.51 5 N 1483 2.21 5 O 1816 1.98 5 H 6501 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 14429 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 576 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "D" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 713 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "E" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1230 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "F" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1300 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1276 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "H" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 786 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain: "I" Number of atoms: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 2811 Classifications: {'DNA': 89} Link IDs: {'rna3p': 88} Chain: "J" Number of atoms: 2838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 2838 Classifications: {'DNA': 89} Link IDs: {'rna3p': 88} Time building chain proxies: 2.57, per 1000 atoms: 0.18 Number of scatterers: 14429 At special positions: 0 Unit cell: (70.84, 118.58, 119.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 178 15.00 O 1816 8.00 N 1483 7.00 C 4437 6.00 H 6501 1.00 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: 1.25 Conformation dependent library (CDL) restraints added in 343.2 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1000 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 76.1% alpha, 2.6% beta 83 base pairs and 154 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.596A pdb=" N LEU A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.527A pdb=" N GLN A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.527A pdb=" N GLY A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.641A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.770A pdb=" N ARG B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 46 through 66 removed outlier: 3.987A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 85 removed outlier: 3.923A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.992A pdb=" N VAL E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA E 115 " --> pdb=" O CYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.694A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 30 Processing helix chain 'F' and resid 31 through 42 removed outlier: 3.540A pdb=" N ILE F 35 " --> pdb=" O THR F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 77 removed outlier: 4.050A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.768A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 38 Processing helix chain 'G' and resid 47 through 73 removed outlier: 3.520A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 56 through 86 removed outlier: 3.591A pdb=" N SER H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.064A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.518A pdb=" N ILE A 120 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.264A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.946A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA7, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.424A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 286 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 210 hydrogen bonds 420 hydrogen bond angles 0 basepair planarities 83 basepair parallelities 154 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6497 1.03 - 1.22: 48 1.22 - 1.42: 3542 1.42 - 1.61: 4812 1.61 - 1.81: 24 Bond restraints: 14923 Sorted by residual: bond pdb=" C3' DA I -5 " pdb=" C2' DA I -5 " ideal model delta sigma weight residual 1.516 1.560 -0.044 8.00e-03 1.56e+04 3.00e+01 bond pdb=" C3' DC I 69 " pdb=" C2' DC I 69 " ideal model delta sigma weight residual 1.516 1.556 -0.040 8.00e-03 1.56e+04 2.51e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.556 -0.040 8.00e-03 1.56e+04 2.44e+01 bond pdb=" C3' DG J -8 " pdb=" C2' DG J -8 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.37e+01 bond pdb=" C3' DA I 61 " pdb=" C2' DA I 61 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.23e+01 ... (remaining 14918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 23783 1.31 - 2.62: 2843 2.62 - 3.92: 292 3.92 - 5.23: 94 5.23 - 6.54: 10 Bond angle restraints: 27022 Sorted by residual: angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 112.90 -4.90 7.00e-01 2.04e+00 4.90e+01 angle pdb=" O4' DT I 34 " pdb=" C1' DT I 34 " pdb=" N1 DT I 34 " ideal model delta sigma weight residual 108.00 112.64 -4.64 7.00e-01 2.04e+00 4.39e+01 angle pdb=" O4' DG I 47 " pdb=" C1' DG I 47 " pdb=" N9 DG I 47 " ideal model delta sigma weight residual 108.00 103.48 4.52 7.00e-01 2.04e+00 4.18e+01 angle pdb=" C4' DC I 21 " pdb=" O4' DC I 21 " pdb=" C1' DC I 21 " ideal model delta sigma weight residual 110.10 103.71 6.39 1.00e+00 1.00e+00 4.09e+01 angle pdb=" C4' DT I 64 " pdb=" O4' DT I 64 " pdb=" C1' DT I 64 " ideal model delta sigma weight residual 110.10 104.65 5.45 1.00e+00 1.00e+00 2.97e+01 ... (remaining 27017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4525 17.62 - 35.24: 753 35.24 - 52.86: 591 52.86 - 70.48: 360 70.48 - 88.11: 14 Dihedral angle restraints: 6243 sinusoidal: 4499 harmonic: 1744 Sorted by residual: dihedral pdb=" CG ARG A 84 " pdb=" CD ARG A 84 " pdb=" NE ARG A 84 " pdb=" CZ ARG A 84 " ideal model delta sinusoidal sigma weight residual -180.00 -136.74 -43.26 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG G 36 " pdb=" CD ARG G 36 " pdb=" NE ARG G 36 " pdb=" CZ ARG G 36 " ideal model delta sinusoidal sigma weight residual -180.00 -136.94 -43.06 2 1.50e+01 4.44e-03 9.94e+00 dihedral pdb=" CG ARG D 93 " pdb=" CD ARG D 93 " pdb=" NE ARG D 93 " pdb=" CZ ARG D 93 " ideal model delta sinusoidal sigma weight residual 90.00 133.02 -43.02 2 1.50e+01 4.44e-03 9.93e+00 ... (remaining 6240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 755 0.039 - 0.079: 378 0.079 - 0.118: 163 0.118 - 0.157: 72 0.157 - 0.197: 18 Chirality restraints: 1386 Sorted by residual: chirality pdb=" C3' DA I 57 " pdb=" C4' DA I 57 " pdb=" O3' DA I 57 " pdb=" C2' DA I 57 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" C3' DA I -14 " pdb=" C4' DA I -14 " pdb=" O3' DA I -14 " pdb=" C2' DA I -14 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" C3' DA I -9 " pdb=" C4' DA I -9 " pdb=" O3' DA I -9 " pdb=" C2' DA I -9 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 1383 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 40 " -0.092 9.50e-02 1.11e+02 4.68e-02 2.89e+01 pdb=" NE ARG F 40 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG F 40 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG F 40 " -0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG F 40 " 0.020 2.00e-02 2.50e+03 pdb="HH11 ARG F 40 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 40 " 0.064 2.00e-02 2.50e+03 pdb="HH21 ARG F 40 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG F 40 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -12 " 0.040 2.00e-02 2.50e+03 2.96e-02 2.42e+01 pdb=" N1 DC I -12 " -0.082 2.00e-02 2.50e+03 pdb=" C2 DC I -12 " 0.035 2.00e-02 2.50e+03 pdb=" O2 DC I -12 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC I -12 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC I -12 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I -12 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DC I -12 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC I -12 " -0.001 2.00e-02 2.50e+03 pdb=" H5 DC I -12 " 0.006 2.00e-02 2.50e+03 pdb=" H6 DC I -12 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 60 " 0.028 2.00e-02 2.50e+03 2.80e-02 2.36e+01 pdb=" N1 DT I 60 " -0.079 2.00e-02 2.50e+03 pdb=" C2 DT I 60 " 0.047 2.00e-02 2.50e+03 pdb=" O2 DT I 60 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 60 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 60 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I 60 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT I 60 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT I 60 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 60 " 0.001 2.00e-02 2.50e+03 pdb=" H3 DT I 60 " -0.005 2.00e-02 2.50e+03 pdb=" H6 DT I 60 " 0.005 2.00e-02 2.50e+03 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 230 2.11 - 2.73: 21092 2.73 - 3.36: 36529 3.36 - 3.98: 46953 3.98 - 4.60: 76162 Nonbonded interactions: 180966 Sorted by model distance: nonbonded pdb=" HG SER A 58 " pdb=" OE1 GLU A 60 " model vdw 1.488 2.450 nonbonded pdb=" O SER A 58 " pdb="HH22 ARG B 41 " model vdw 1.610 2.450 nonbonded pdb=" HG1 THR F 74 " pdb=" OD2 ASP F 86 " model vdw 1.627 2.450 nonbonded pdb=" OE2 GLU C 42 " pdb=" HG SER D 88 " model vdw 1.639 2.450 nonbonded pdb=" OE2 GLU F 53 " pdb="HH11 ARG F 56 " model vdw 1.653 2.450 ... (remaining 180961 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 'B' and resid 25 through 101) selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 60 through 103) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.960 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 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 : 0.007 0.065 8422 Z= 0.608 Angle : 0.998 6.539 12124 Z= 0.842 Chirality : 0.060 0.197 1386 Planarity : 0.012 0.098 916 Dihedral : 26.107 88.105 3610 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.22 % Allowed : 7.19 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.32), residues: 520 helix: 0.98 (0.23), residues: 390 sheet: None (None), residues: 0 loop : -0.68 (0.42), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.004 ARG F 40 TYR 0.021 0.004 TYR A 100 PHE 0.019 0.003 PHE E 105 HIS 0.011 0.003 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.61 ( 8422) covalent geometry : angle 0.99804 / 0.84 (12124) hydrogen bonds : bond 0.12832 / 8.86 ( 496) hydrogen bonds : angle 4.10368 / 3.07 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.261 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6073 (m-80) cc_final: 0.5447 (m-10) REVERT: F 92 LYS cc_start: 0.8256 (tptm) cc_final: 0.8046 (tppp) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.3174 time to fit residues: 68.9633 Evaluate side-chains 114 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN F 76 HIS G 74 ASN H 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.113638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.096267 restraints weight = 70370.384| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.29 r_work: 0.3740 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8422 Z= 0.236 Angle : 0.768 6.202 12124 Z= 0.490 Chirality : 0.049 0.214 1386 Planarity : 0.006 0.048 916 Dihedral : 29.011 87.009 2553 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.35 % Allowed : 14.38 % Favored : 84.27 % 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: 1.30 (0.33), residues: 520 helix: 1.55 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -1.37 (0.42), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 132 TYR 0.018 0.002 TYR A 100 PHE 0.012 0.002 PHE D 66 HIS 0.013 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.24 ( 8422) covalent geometry : angle 0.76753 / 0.49 (12124) hydrogen bonds : bond 0.08537 / 5.86 ( 496) hydrogen bonds : angle 3.91241 / 2.87 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.318 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: symmetry clash REVERT: F 79 ARG cc_start: 0.6891 (mmm160) cc_final: 0.5786 (mtm110) outliers start: 6 outliers final: 4 residues processed: 126 average time/residue: 0.3322 time to fit residues: 50.2871 Evaluate side-chains 116 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 79 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.111821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.094480 restraints weight = 72409.199| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 3.28 r_work: 0.3703 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8422 Z= 0.217 Angle : 0.696 5.025 12124 Z= 0.460 Chirality : 0.044 0.163 1386 Planarity : 0.005 0.036 916 Dihedral : 29.107 86.529 2553 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.25 % Allowed : 15.28 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.34), residues: 520 helix: 1.30 (0.24), residues: 398 sheet: None (None), residues: 0 loop : -1.78 (0.41), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 132 TYR 0.020 0.002 TYR A 100 PHE 0.010 0.002 PHE H 71 HIS 0.007 0.002 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.22 ( 8422) covalent geometry : angle 0.69628 / 0.46 (12124) hydrogen bonds : bond 0.08248 / 5.61 ( 496) hydrogen bonds : angle 3.81828 / 2.80 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.324 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: symmetry clash revert: symmetry clash REVERT: D 87 ARG cc_start: 0.6803 (tpp80) cc_final: 0.6396 (tpp80) REVERT: E 91 MET cc_start: 0.5214 (ppp) cc_final: 0.4971 (ppp) REVERT: F 79 ARG cc_start: 0.6922 (mmm160) cc_final: 0.5992 (mtm110) REVERT: H 94 GLU cc_start: 0.8284 (mp0) cc_final: 0.7523 (mt-10) outliers start: 10 outliers final: 9 residues processed: 120 average time/residue: 0.3009 time to fit residues: 43.9429 Evaluate side-chains 116 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 79 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.112405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.094820 restraints weight = 71758.208| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.31 r_work: 0.3721 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8422 Z= 0.171 Angle : 0.652 6.890 12124 Z= 0.428 Chirality : 0.043 0.165 1386 Planarity : 0.004 0.034 916 Dihedral : 29.099 87.485 2553 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.47 % Allowed : 16.18 % Favored : 81.35 % 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: 1.17 (0.34), residues: 520 helix: 1.59 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -2.01 (0.41), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 132 TYR 0.015 0.001 TYR A 100 PHE 0.010 0.002 PHE D 66 HIS 0.005 0.002 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.17 ( 8422) covalent geometry : angle 0.65204 / 0.43 (12124) hydrogen bonds : bond 0.07052 / 4.79 ( 496) hydrogen bonds : angle 3.51218 / 2.58 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.330 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: C 35 LEU cc_start: 0.8710 (mt) cc_final: 0.8502 (mt) REVERT: D 87 ARG cc_start: 0.6797 (tpp80) cc_final: 0.6406 (tpp80) REVERT: H 93 ARG cc_start: 0.6747 (mmp80) cc_final: 0.6342 (mmp80) REVERT: H 94 GLU cc_start: 0.8294 (mp0) cc_final: 0.7562 (mm-30) outliers start: 11 outliers final: 10 residues processed: 114 average time/residue: 0.3161 time to fit residues: 43.5843 Evaluate side-chains 115 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 73 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.0000 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.112265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.094453 restraints weight = 72063.298| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.33 r_work: 0.3717 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8422 Z= 0.172 Angle : 0.642 5.897 12124 Z= 0.424 Chirality : 0.042 0.151 1386 Planarity : 0.005 0.050 916 Dihedral : 29.066 88.843 2553 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.92 % Allowed : 16.40 % Favored : 80.67 % 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: 1.23 (0.35), residues: 520 helix: 1.67 (0.25), residues: 395 sheet: None (None), residues: 0 loop : -2.03 (0.42), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 132 TYR 0.015 0.001 TYR A 100 PHE 0.011 0.001 PHE D 66 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.17 ( 8422) covalent geometry : angle 0.64233 / 0.42 (12124) hydrogen bonds : bond 0.06785 / 4.60 ( 496) hydrogen bonds : angle 3.45962 / 2.54 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.344 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: C 35 LEU cc_start: 0.8710 (mt) cc_final: 0.8490 (mt) REVERT: E 91 MET cc_start: 0.5211 (ppp) cc_final: 0.4989 (ppp) REVERT: F 79 ARG cc_start: 0.6922 (mmm-85) cc_final: 0.6237 (mtm110) REVERT: G 74 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7748 (t0) REVERT: H 94 GLU cc_start: 0.8238 (mp0) cc_final: 0.7519 (mm-30) outliers start: 13 outliers final: 10 residues processed: 115 average time/residue: 0.3070 time to fit residues: 42.6382 Evaluate side-chains 114 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 79 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.107971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.090476 restraints weight = 72487.233| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.33 r_work: 0.3624 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8422 Z= 0.321 Angle : 0.802 6.351 12124 Z= 0.502 Chirality : 0.047 0.185 1386 Planarity : 0.006 0.049 916 Dihedral : 29.198 88.553 2553 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.27 % Allowed : 17.08 % Favored : 78.65 % 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: -0.90 (0.34), residues: 520 helix: 0.08 (0.24), residues: 393 sheet: None (None), residues: 0 loop : -2.54 (0.46), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 30 TYR 0.032 0.002 TYR A 100 PHE 0.014 0.003 PHE D 66 HIS 0.015 0.004 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.32 ( 8422) covalent geometry : angle 0.80165 / 0.50 (12124) hydrogen bonds : bond 0.10147 / 6.83 ( 496) hydrogen bonds : angle 4.46081 / 3.27 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8347 (tttp) cc_final: 0.8037 (ttmt) REVERT: C 35 LEU cc_start: 0.8733 (mt) cc_final: 0.8520 (mt) REVERT: H 94 GLU cc_start: 0.8350 (mp0) cc_final: 0.7592 (mm-30) outliers start: 19 outliers final: 16 residues processed: 112 average time/residue: 0.2942 time to fit residues: 40.0014 Evaluate side-chains 115 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.109989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.092018 restraints weight = 72243.596| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 3.31 r_work: 0.3675 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8422 Z= 0.177 Angle : 0.662 7.244 12124 Z= 0.432 Chirality : 0.042 0.162 1386 Planarity : 0.005 0.052 916 Dihedral : 29.084 89.298 2553 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.82 % Allowed : 18.43 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.35), residues: 520 helix: 0.78 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -2.36 (0.48), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 93 TYR 0.018 0.001 TYR A 100 PHE 0.012 0.002 PHE A 105 HIS 0.009 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.18 ( 8422) covalent geometry : angle 0.66196 / 0.43 (12124) hydrogen bonds : bond 0.07513 / 5.02 ( 496) hydrogen bonds : angle 3.76465 / 2.76 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 LEU cc_start: 0.8719 (mt) cc_final: 0.8504 (mt) REVERT: G 74 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.8046 (t0) REVERT: G 93 GLU cc_start: 0.6672 (tp30) cc_final: 0.6385 (mp0) REVERT: H 94 GLU cc_start: 0.8249 (mp0) cc_final: 0.7616 (mm-30) outliers start: 17 outliers final: 14 residues processed: 112 average time/residue: 0.2965 time to fit residues: 40.3397 Evaluate side-chains 113 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 59 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.110519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.092637 restraints weight = 72536.351| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 3.32 r_work: 0.3688 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8422 Z= 0.175 Angle : 0.651 7.224 12124 Z= 0.422 Chirality : 0.042 0.223 1386 Planarity : 0.005 0.064 916 Dihedral : 28.952 89.693 2553 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.60 % Allowed : 18.43 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.36), residues: 520 helix: 1.22 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -2.28 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 36 TYR 0.016 0.001 TYR A 100 PHE 0.010 0.002 PHE D 66 HIS 0.005 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.17 ( 8422) covalent geometry : angle 0.65100 / 0.42 (12124) hydrogen bonds : bond 0.06736 / 4.50 ( 496) hydrogen bonds : angle 3.56504 / 2.61 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8321 (tttp) cc_final: 0.7995 (ttmt) REVERT: C 35 LEU cc_start: 0.8718 (mt) cc_final: 0.8503 (mt) REVERT: G 74 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8092 (t0) REVERT: H 80 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7505 (mmm160) REVERT: H 94 GLU cc_start: 0.8237 (mp0) cc_final: 0.7548 (mm-30) outliers start: 16 outliers final: 15 residues processed: 108 average time/residue: 0.3066 time to fit residues: 40.3542 Evaluate side-chains 110 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.108963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.091298 restraints weight = 72021.374| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 3.35 r_work: 0.3651 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8422 Z= 0.210 Angle : 0.685 7.669 12124 Z= 0.437 Chirality : 0.042 0.175 1386 Planarity : 0.005 0.047 916 Dihedral : 28.980 89.424 2553 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.15 % Allowed : 19.55 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.35), residues: 520 helix: 0.85 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -2.44 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG G 36 TYR 0.022 0.002 TYR A 100 PHE 0.013 0.002 PHE D 66 HIS 0.004 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.21 ( 8422) covalent geometry : angle 0.68510 / 0.44 (12124) hydrogen bonds : bond 0.07595 / 5.08 ( 496) hydrogen bonds : angle 3.82942 / 2.80 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8387 (tttp) cc_final: 0.8059 (ttmt) REVERT: B 85 MET cc_start: 0.4349 (mmp) cc_final: 0.3717 (mmp) REVERT: C 35 LEU cc_start: 0.8750 (mt) cc_final: 0.8541 (mt) REVERT: D 87 ARG cc_start: 0.6965 (tpp80) cc_final: 0.6657 (tpp80) REVERT: G 74 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8088 (t0) REVERT: H 94 GLU cc_start: 0.8230 (mp0) cc_final: 0.7477 (mm-30) outliers start: 14 outliers final: 13 residues processed: 109 average time/residue: 0.2834 time to fit residues: 37.5276 Evaluate side-chains 111 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.110836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.093157 restraints weight = 70798.041| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.29 r_work: 0.3684 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8422 Z= 0.157 Angle : 0.632 7.375 12124 Z= 0.409 Chirality : 0.041 0.193 1386 Planarity : 0.005 0.061 916 Dihedral : 28.945 89.101 2553 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.15 % Allowed : 19.55 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.36), residues: 520 helix: 1.41 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -2.21 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 36 TYR 0.011 0.001 TYR A 100 PHE 0.010 0.001 PHE D 66 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.16 ( 8422) covalent geometry : angle 0.63237 / 0.41 (12124) hydrogen bonds : bond 0.06224 / 4.14 ( 496) hydrogen bonds : angle 3.42342 / 2.51 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8369 (tttp) cc_final: 0.8135 (ttmt) REVERT: B 85 MET cc_start: 0.4256 (mmp) cc_final: 0.3607 (mmp) REVERT: C 35 LEU cc_start: 0.8737 (mt) cc_final: 0.8523 (mt) REVERT: G 74 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8048 (t0) REVERT: H 94 GLU cc_start: 0.8195 (mp0) cc_final: 0.7497 (mm-30) outliers start: 14 outliers final: 13 residues processed: 110 average time/residue: 0.2761 time to fit residues: 37.3513 Evaluate side-chains 111 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 overall best weight: 1.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.111334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.093821 restraints weight = 71252.598| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.27 r_work: 0.3696 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8422 Z= 0.158 Angle : 0.634 7.191 12124 Z= 0.406 Chirality : 0.040 0.195 1386 Planarity : 0.004 0.048 916 Dihedral : 28.922 88.124 2553 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.47 % Allowed : 20.22 % Favored : 77.30 % 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: 1.03 (0.36), residues: 520 helix: 1.57 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -2.16 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 36 TYR 0.013 0.001 TYR A 100 PHE 0.010 0.001 PHE D 66 HIS 0.007 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.16 ( 8422) covalent geometry : angle 0.63364 / 0.41 (12124) hydrogen bonds : bond 0.05968 / 3.98 ( 496) hydrogen bonds : angle 3.33707 / 2.45 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3589.31 seconds wall clock time: 61 minutes 33.99 seconds (3693.99 seconds total)