Starting phenix.real_space_refine on Fri Jul 3 14:33:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmt_48403/07_2026/9mmt_48403.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmt_48403/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mmt_48403/07_2026/9mmt_48403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmt_48403/07_2026/9mmt_48403.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmt_48403/07_2026/9mmt_48403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmt_48403/07_2026/9mmt_48403.cif" } 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-dev-6108/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: 2.73, per 1000 atoms: 0.19 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: 1.02 Conformation dependent library (CDL) restraints added in 451.4 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: 2.47 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: 3.35 Time building geometry restraints manager: 1.61 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: 23829 1.31 - 2.62: 2808 2.62 - 3.92: 281 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: 6.070 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: 0.060 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.380 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- 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 : 0.989 6.539 12124 Z= 0.832 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 0.98859 / 0.83 (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 : 0.297 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: A 79 PHE cc_start: 0.6073 (m-80) cc_final: 0.5445 (m-10) REVERT: F 92 LYS cc_start: 0.8256 (tptm) cc_final: 0.8045 (tppp) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.2919 time to fit residues: 63.2722 Evaluate side-chains 113 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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: 9.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 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 = 0.113653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.096350 restraints weight = 70839.830| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.30 r_work: 0.3738 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8422 Z= 0.237 Angle : 0.767 5.891 12124 Z= 0.491 Chirality : 0.050 0.230 1386 Planarity : 0.006 0.049 916 Dihedral : 29.025 86.902 2553 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.35 % Allowed : 14.16 % Favored : 84.49 % 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: 1.24 (0.33), residues: 520 helix: 1.51 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 132 TYR 0.018 0.002 TYR A 100 PHE 0.011 0.002 PHE D 66 HIS 0.013 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.24 ( 8422) covalent geometry : angle 0.76675 / 0.49 (12124) hydrogen bonds : bond 0.08555 / 5.86 ( 496) hydrogen bonds : angle 3.91199 / 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 : 0.180 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 outliers start: 6 outliers final: 4 residues processed: 126 average time/residue: 0.2796 time to fit residues: 42.2581 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 : 0.309 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 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: 2.8784 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.111368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.094007 restraints weight = 72205.750| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.24 r_work: 0.3704 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8422 Z= 0.226 Angle : 0.694 4.795 12124 Z= 0.462 Chirality : 0.044 0.160 1386 Planarity : 0.005 0.035 916 Dihedral : 29.122 86.518 2553 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.02 % Allowed : 15.28 % Favored : 82.70 % 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: 0.83 (0.34), residues: 520 helix: 1.25 (0.24), residues: 398 sheet: None (None), residues: 0 loop : -1.74 (0.42), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 132 TYR 0.020 0.001 TYR A 100 PHE 0.011 0.002 PHE H 71 HIS 0.008 0.002 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.23 ( 8422) covalent geometry : angle 0.69443 / 0.46 (12124) hydrogen bonds : bond 0.08385 / 5.70 ( 496) hydrogen bonds : angle 3.86714 / 2.84 ( 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: 9 poor density : 115 time to evaluate : 0.329 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: D 87 ARG cc_start: 0.6791 (tpp80) cc_final: 0.6385 (tpp80) REVERT: H 94 GLU cc_start: 0.8280 (mp0) cc_final: 0.7506 (mt-10) outliers start: 9 outliers final: 8 residues processed: 120 average time/residue: 0.2831 time to fit residues: 41.2617 Evaluate side-chains 117 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain D residue 88 SER 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: 0.9980 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.112667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.095097 restraints weight = 70690.723| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.27 r_work: 0.3726 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4178 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= 0.164 Angle : 0.643 5.640 12124 Z= 0.426 Chirality : 0.042 0.170 1386 Planarity : 0.004 0.034 916 Dihedral : 29.117 87.382 2553 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.80 % Allowed : 16.18 % Favored : 82.02 % 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: 1.26 (0.35), residues: 520 helix: 1.66 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -2.03 (0.41), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 132 TYR 0.013 0.001 TYR A 100 PHE 0.010 0.001 PHE D 66 HIS 0.004 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.16 ( 8422) covalent geometry : angle 0.64278 / 0.43 (12124) hydrogen bonds : bond 0.06979 / 4.74 ( 496) hydrogen bonds : angle 3.46332 / 2.55 ( 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 113 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.216 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 80 LYS cc_start: 0.8155 (tttp) cc_final: 0.7917 (ttmt) REVERT: C 35 LEU cc_start: 0.8691 (mt) cc_final: 0.8471 (mt) REVERT: D 87 ARG cc_start: 0.6799 (tpp80) cc_final: 0.6404 (tpp80) REVERT: E 91 MET cc_start: 0.5192 (ppp) cc_final: 0.4971 (ppp) REVERT: H 93 ARG cc_start: 0.6741 (mmp80) cc_final: 0.6331 (mmp80) REVERT: H 94 GLU cc_start: 0.8273 (mp0) cc_final: 0.7559 (mm-30) outliers start: 8 outliers final: 8 residues processed: 108 average time/residue: 0.2864 time to fit residues: 36.9955 Evaluate side-chains 108 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.111648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.093862 restraints weight = 71962.345| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.35 r_work: 0.3700 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8422 Z= 0.186 Angle : 0.650 5.530 12124 Z= 0.429 Chirality : 0.042 0.146 1386 Planarity : 0.005 0.045 916 Dihedral : 29.104 88.504 2553 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.47 % Allowed : 16.63 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.34), residues: 520 helix: 1.57 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -1.97 (0.42), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 117 TYR 0.016 0.001 TYR A 100 PHE 0.012 0.002 PHE D 66 HIS 0.014 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.19 ( 8422) covalent geometry : angle 0.65020 / 0.43 (12124) hydrogen bonds : bond 0.07121 / 4.83 ( 496) hydrogen bonds : angle 3.57955 / 2.63 ( 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 118 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.313 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: C 35 LEU cc_start: 0.8704 (mt) cc_final: 0.8480 (mt) REVERT: H 93 ARG cc_start: 0.6791 (mmp80) cc_final: 0.6361 (mmp80) REVERT: H 94 GLU cc_start: 0.8275 (mp0) cc_final: 0.7527 (mm-30) outliers start: 11 outliers final: 11 residues processed: 112 average time/residue: 0.3039 time to fit residues: 40.8686 Evaluate side-chains 117 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 F residue 74 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 64 LEU 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: 10.0000 chunk 58 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** 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 = 0.4121 r_free = 0.4121 target = 0.107101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.089643 restraints weight = 72688.835| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.32 r_work: 0.3603 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 8422 Z= 0.339 Angle : 0.838 6.342 12124 Z= 0.522 Chirality : 0.049 0.203 1386 Planarity : 0.007 0.047 916 Dihedral : 29.312 88.254 2553 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.49 % Allowed : 15.51 % Favored : 80.00 % 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: -1.45 (0.33), residues: 520 helix: -0.30 (0.24), residues: 393 sheet: None (None), residues: 0 loop : -2.80 (0.45), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 30 TYR 0.038 0.003 TYR A 100 PHE 0.017 0.003 PHE A 105 HIS 0.010 0.003 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.34 ( 8422) covalent geometry : angle 0.83802 / 0.52 (12124) hydrogen bonds : bond 0.11205 / 7.54 ( 496) hydrogen bonds : angle 4.73218 / 3.45 ( 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 126 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.313 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: A 80 LYS cc_start: 0.8343 (tttp) cc_final: 0.8021 (ttmt) REVERT: C 35 LEU cc_start: 0.8741 (mt) cc_final: 0.8531 (mt) REVERT: H 93 ARG cc_start: 0.7023 (mmp80) cc_final: 0.6575 (mmp80) REVERT: H 94 GLU cc_start: 0.8413 (mp0) cc_final: 0.7603 (mm-30) outliers start: 20 outliers final: 17 residues processed: 117 average time/residue: 0.2997 time to fit residues: 42.2773 Evaluate side-chains 115 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 G residue 108 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 79 SER 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: 3.9990 chunk 60 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.109281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.091380 restraints weight = 72498.290| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.32 r_work: 0.3662 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8422 Z= 0.190 Angle : 0.673 7.391 12124 Z= 0.438 Chirality : 0.043 0.178 1386 Planarity : 0.005 0.045 916 Dihedral : 29.202 89.032 2553 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.82 % Allowed : 17.53 % 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: -0.36 (0.35), residues: 520 helix: 0.51 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -2.48 (0.47), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 132 TYR 0.017 0.001 TYR A 100 PHE 0.011 0.002 PHE A 105 HIS 0.005 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.19 ( 8422) covalent geometry : angle 0.67268 / 0.44 (12124) hydrogen bonds : bond 0.07881 / 5.26 ( 496) hydrogen bonds : angle 3.93467 / 2.89 ( 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 123 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8335 (tttp) cc_final: 0.8012 (ttmt) REVERT: C 35 LEU cc_start: 0.8724 (mt) cc_final: 0.8510 (mt) REVERT: G 93 GLU cc_start: 0.6732 (tp30) cc_final: 0.6404 (mp0) REVERT: H 93 ARG cc_start: 0.6858 (mmp80) cc_final: 0.6426 (mmp80) REVERT: H 94 GLU cc_start: 0.8294 (mp0) cc_final: 0.7612 (mm-30) outliers start: 17 outliers final: 14 residues processed: 117 average time/residue: 0.2919 time to fit residues: 41.2539 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 : 0.297 ------------------------------------------------------------------------------- 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 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 H residue 79 SER 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: 3.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.110065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.092150 restraints weight = 72226.296| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.32 r_work: 0.3681 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8422 Z= 0.171 Angle : 0.650 7.218 12124 Z= 0.423 Chirality : 0.042 0.181 1386 Planarity : 0.005 0.062 916 Dihedral : 29.088 89.816 2553 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.15 % Allowed : 19.10 % 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: 0.27 (0.35), residues: 520 helix: 0.99 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -2.35 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 36 TYR 0.022 0.002 TYR B 89 PHE 0.010 0.002 PHE D 66 HIS 0.013 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.17 ( 8422) covalent geometry : angle 0.64988 / 0.42 (12124) hydrogen bonds : bond 0.07026 / 4.69 ( 496) hydrogen bonds : angle 3.62036 / 2.66 ( 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 112 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8323 (tttp) cc_final: 0.8005 (ttmt) REVERT: C 35 LEU cc_start: 0.8729 (mt) cc_final: 0.8516 (mt) REVERT: G 74 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8092 (t0) REVERT: G 93 GLU cc_start: 0.6701 (tp30) cc_final: 0.6378 (mp0) REVERT: H 93 ARG cc_start: 0.6831 (mmp80) cc_final: 0.6379 (mmp80) REVERT: H 94 GLU cc_start: 0.8293 (mp0) cc_final: 0.7586 (mm-30) outliers start: 14 outliers final: 12 residues processed: 107 average time/residue: 0.2921 time to fit residues: 37.7446 Evaluate side-chains 108 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain G residue 74 ASN 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: 1.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.109733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.091948 restraints weight = 72266.454| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.39 r_work: 0.3661 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8422 Z= 0.180 Angle : 0.647 7.221 12124 Z= 0.419 Chirality : 0.041 0.192 1386 Planarity : 0.005 0.048 916 Dihedral : 29.040 89.508 2553 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.37 % Allowed : 19.55 % Favored : 77.08 % 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: 0.32 (0.35), residues: 520 helix: 1.03 (0.25), residues: 395 sheet: None (None), residues: 0 loop : -2.42 (0.50), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 36 TYR 0.022 0.002 TYR B 89 PHE 0.011 0.002 PHE D 66 HIS 0.007 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 ( 8422) covalent geometry : angle 0.64700 / 0.42 (12124) hydrogen bonds : bond 0.06991 / 4.66 ( 496) hydrogen bonds : angle 3.62056 / 2.65 ( 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: 15 poor density : 100 time to evaluate : 0.311 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: 0.8368 (tttp) cc_final: 0.8027 (ttmt) REVERT: C 35 LEU cc_start: 0.8746 (mt) cc_final: 0.8537 (mt) REVERT: D 87 ARG cc_start: 0.6992 (tpp80) cc_final: 0.6710 (tpp80) REVERT: G 43 ARG cc_start: 0.8325 (mtp-110) cc_final: 0.8063 (mtp85) REVERT: G 74 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8059 (t0) REVERT: H 93 ARG cc_start: 0.6868 (mmp80) cc_final: 0.6406 (mmp80) REVERT: H 94 GLU cc_start: 0.8249 (mp0) cc_final: 0.7528 (mm-30) outliers start: 15 outliers final: 14 residues processed: 108 average time/residue: 0.2940 time to fit residues: 38.3609 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 : 0.344 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL 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: 0.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.109117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.091387 restraints weight = 71327.016| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.35 r_work: 0.3656 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8422 Z= 0.193 Angle : 0.655 7.217 12124 Z= 0.422 Chirality : 0.041 0.185 1386 Planarity : 0.006 0.079 916 Dihedral : 29.041 89.309 2553 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.60 % Allowed : 19.10 % 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: 0.22 (0.36), residues: 520 helix: 0.96 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -2.33 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 68 TYR 0.024 0.002 TYR B 89 PHE 0.013 0.002 PHE D 66 HIS 0.010 0.002 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.19 ( 8422) covalent geometry : angle 0.65502 / 0.42 (12124) hydrogen bonds : bond 0.07183 / 4.79 ( 496) hydrogen bonds : angle 3.72087 / 2.72 ( 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 114 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.305 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 80 LYS cc_start: 0.8412 (tttp) cc_final: 0.8067 (ttmt) REVERT: B 85 MET cc_start: 0.4484 (mmp) cc_final: 0.4039 (mmp) REVERT: C 35 LEU cc_start: 0.8736 (mt) cc_final: 0.8530 (mt) REVERT: D 87 ARG cc_start: 0.7116 (tpp80) cc_final: 0.6821 (tpp80) REVERT: G 74 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8098 (t0) REVERT: H 93 ARG cc_start: 0.6869 (mmp80) cc_final: 0.6397 (mmp80) REVERT: H 94 GLU cc_start: 0.8247 (mp0) cc_final: 0.7516 (mm-30) outliers start: 16 outliers final: 15 residues processed: 107 average time/residue: 0.2938 time to fit residues: 37.8122 Evaluate side-chains 114 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain H residue 99 VAL 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: 3.9990 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: 9.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.109717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.092107 restraints weight = 71447.297| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.30 r_work: 0.3662 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8422 Z= 0.179 Angle : 0.636 7.298 12124 Z= 0.412 Chirality : 0.040 0.196 1386 Planarity : 0.005 0.050 916 Dihedral : 29.058 89.214 2553 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.37 % Allowed : 19.33 % 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: 0.44 (0.36), residues: 520 helix: 1.11 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -2.21 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 36 TYR 0.018 0.001 TYR B 89 PHE 0.010 0.002 PHE D 66 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 ( 8422) covalent geometry : angle 0.63637 / 0.41 (12124) hydrogen bonds : bond 0.06842 / 4.54 ( 496) hydrogen bonds : angle 3.62001 / 2.65 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3312.10 seconds wall clock time: 56 minutes 58.39 seconds (3418.39 seconds total)