Starting phenix.real_space_refine on Thu Feb 5 02:18:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmt_48403/02_2026/9mmt_48403.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmt_48403/02_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_48403/02_2026/9mmt_48403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmt_48403/02_2026/9mmt_48403.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mmt_48403/02_2026/9mmt_48403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmt_48403/02_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-2.0-5952/lib/python3.9/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: 2.71, 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: 1.00 Conformation dependent library (CDL) restraints added in 303.3 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: 2.98 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: 2.58 Time building geometry restraints manager: 1.41 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=" N ARG F 24 " pdb=" CA ARG F 24 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" C3' DA I -5 " pdb=" C2' DA I -5 " ideal model delta sigma weight residual 1.525 1.560 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" N ASP B 25 " pdb=" CA ASP B 25 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" C3' DC I 69 " pdb=" C2' DC I 69 " ideal model delta sigma weight residual 1.525 1.556 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" N ARG F 24 " pdb=" H ARG F 24 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 14918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 24026 1.31 - 2.62: 2717 2.62 - 3.92: 251 3.92 - 5.23: 26 5.23 - 6.54: 2 Bond angle restraints: 27022 Sorted by residual: angle pdb=" C4' DC I 21 " pdb=" O4' DC I 21 " pdb=" C1' DC I 21 " ideal model delta sigma weight residual 109.70 103.71 5.99 1.50e+00 4.44e-01 1.60e+01 angle pdb=" C4' DT I 64 " pdb=" O4' DT I 64 " pdb=" C1' DT I 64 " ideal model delta sigma weight residual 109.70 104.65 5.05 1.50e+00 4.44e-01 1.13e+01 angle pdb=" C2' DG I 54 " pdb=" C1' DG I 54 " pdb=" N9 DG I 54 " ideal model delta sigma weight residual 113.50 118.46 -4.96 1.50e+00 4.44e-01 1.09e+01 angle pdb=" O4' DG I 47 " pdb=" C1' DG I 47 " pdb=" N9 DG I 47 " ideal model delta sigma weight residual 108.40 103.48 4.92 1.50e+00 4.44e-01 1.08e+01 angle pdb=" C2' DG J -8 " pdb=" C1' DG J -8 " pdb=" N9 DG J -8 " ideal model delta sigma weight residual 113.50 118.40 -4.90 1.50e+00 4.44e-01 1.07e+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 - 0.035: 802 0.035 - 0.071: 396 0.071 - 0.106: 140 0.106 - 0.141: 37 0.141 - 0.176: 11 Chirality restraints: 1386 Sorted by residual: chirality pdb=" C1' DC I 66 " pdb=" O4' DC I 66 " pdb=" C2' DC I 66 " pdb=" N1 DC I 66 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" C4' DC I 21 " pdb=" C5' DC I 21 " pdb=" O4' DC I 21 " pdb=" C3' DC I 21 " both_signs ideal model delta sigma weight residual False -2.53 -2.36 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" C1' DG I 20 " pdb=" O4' DG I 20 " pdb=" C2' DG I 20 " pdb=" N9 DG I 20 " both_signs ideal model delta sigma weight residual False 2.42 2.26 0.16 2.00e-01 2.50e+01 6.75e-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: 5.130 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: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.390 Find NCS groups from input model: 0.060 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8422 Z= 0.245 Angle : 0.884 6.539 12124 Z= 0.567 Chirality : 0.048 0.176 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 covalent geometry : bond 0.00528 ( 8422) covalent geometry : angle 0.88437 (12124) hydrogen bonds : bond 0.12832 ( 496) hydrogen bonds : angle 4.10368 ( 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 : 0.296 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: 0.3364 time to fit residues: 71.6256 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 : 0.238 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4202 r_free = 0.4202 target = 0.111889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.094341 restraints weight = 70926.631| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.30 r_work: 0.3702 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8422 Z= 0.241 Angle : 0.714 4.800 12124 Z= 0.441 Chirality : 0.042 0.134 1386 Planarity : 0.005 0.040 916 Dihedral : 28.816 86.233 2553 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 1.44 (0.34), residues: 520 helix: 1.73 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -1.62 (0.40), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 132 TYR 0.020 0.002 TYR A 100 PHE 0.012 0.002 PHE A 105 HIS 0.008 0.002 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 8422) covalent geometry : angle 0.71357 (12124) hydrogen bonds : bond 0.07860 ( 496) hydrogen bonds : angle 3.60072 ( 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 132 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.199 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: F 36 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.8347 (mmm-85) REVERT: H 93 ARG cc_start: 0.6690 (mmp80) cc_final: 0.6294 (mmp80) REVERT: H 94 GLU cc_start: 0.8168 (mp0) cc_final: 0.7615 (mt-10) outliers start: 6 outliers final: 5 residues processed: 129 average time/residue: 0.3009 time to fit residues: 45.9538 Evaluate side-chains 113 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 ASN E 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.113419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.095843 restraints weight = 71070.936| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.30 r_work: 0.3746 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8422 Z= 0.177 Angle : 0.643 4.979 12124 Z= 0.401 Chirality : 0.038 0.138 1386 Planarity : 0.004 0.034 916 Dihedral : 28.549 89.365 2553 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.80 % Allowed : 15.96 % Favored : 82.25 % 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: 1.96 (0.35), residues: 520 helix: 2.21 (0.25), residues: 396 sheet: None (None), residues: 0 loop : -1.87 (0.40), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 132 TYR 0.011 0.001 TYR A 100 PHE 0.010 0.001 PHE D 66 HIS 0.007 0.001 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8422) covalent geometry : angle 0.64289 (12124) hydrogen bonds : bond 0.05493 ( 496) hydrogen bonds : angle 3.13618 ( 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 117 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.285 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: B 36 ARG cc_start: 0.9028 (mtt-85) cc_final: 0.8648 (mtt-85) REVERT: C 35 LEU cc_start: 0.8750 (mt) cc_final: 0.8518 (mt) REVERT: E 91 MET cc_start: 0.5044 (ppp) cc_final: 0.4787 (ppp) REVERT: G 43 ARG cc_start: 0.8255 (mtp-110) cc_final: 0.7975 (mtp-110) REVERT: H 93 ARG cc_start: 0.6687 (mmp80) cc_final: 0.6414 (mmp80) REVERT: H 94 GLU cc_start: 0.8103 (mp0) cc_final: 0.7610 (mt-10) outliers start: 8 outliers final: 6 residues processed: 113 average time/residue: 0.3659 time to fit residues: 48.0745 Evaluate side-chains 108 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 108 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.113178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.095706 restraints weight = 70801.683| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.37 r_work: 0.3729 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8422 Z= 0.172 Angle : 0.617 4.346 12124 Z= 0.385 Chirality : 0.038 0.136 1386 Planarity : 0.004 0.042 916 Dihedral : 28.420 89.572 2553 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.80 % Allowed : 15.96 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.36), residues: 520 helix: 2.31 (0.25), residues: 394 sheet: None (None), residues: 0 loop : -1.90 (0.41), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 36 TYR 0.012 0.001 TYR A 100 PHE 0.009 0.001 PHE D 71 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8422) covalent geometry : angle 0.61702 (12124) hydrogen bonds : bond 0.05061 ( 496) hydrogen bonds : angle 3.05198 ( 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 : 0.243 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: B 36 ARG cc_start: 0.9052 (mtt-85) cc_final: 0.8688 (mtt-85) REVERT: D 87 ARG cc_start: 0.6868 (tpp80) cc_final: 0.6537 (tpp80) REVERT: H 93 ARG cc_start: 0.6640 (mmp80) cc_final: 0.6351 (mmp80) REVERT: H 94 GLU cc_start: 0.8035 (mp0) cc_final: 0.7578 (mm-30) outliers start: 8 outliers final: 7 residues processed: 110 average time/residue: 0.2921 time to fit residues: 38.0235 Evaluate side-chains 105 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 SER 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 H residue 101 LEU 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: 0.6980 chunk 47 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.112061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.094395 restraints weight = 70197.947| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.38 r_work: 0.3706 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8422 Z= 0.182 Angle : 0.617 4.427 12124 Z= 0.384 Chirality : 0.039 0.142 1386 Planarity : 0.004 0.042 916 Dihedral : 28.372 88.114 2553 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: 1.73 (0.35), residues: 520 helix: 2.07 (0.25), residues: 394 sheet: None (None), residues: 0 loop : -1.99 (0.43), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 36 TYR 0.020 0.001 TYR A 100 PHE 0.009 0.001 PHE D 71 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8422) covalent geometry : angle 0.61677 (12124) hydrogen bonds : bond 0.05443 ( 496) hydrogen bonds : angle 3.16614 ( 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 : 0.250 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: A 80 LYS cc_start: 0.8303 (tttp) cc_final: 0.7995 (ttmt) REVERT: B 36 ARG cc_start: 0.9050 (mtt-85) cc_final: 0.8668 (mtt-85) REVERT: D 87 ARG cc_start: 0.6920 (tpp80) cc_final: 0.6563 (tpp80) REVERT: H 93 ARG cc_start: 0.6646 (mmp80) cc_final: 0.6345 (mmp80) REVERT: H 94 GLU cc_start: 0.8076 (mp0) cc_final: 0.7606 (mm-30) outliers start: 11 outliers final: 11 residues processed: 114 average time/residue: 0.3382 time to fit residues: 45.5258 Evaluate side-chains 111 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 59 LEU Chi-restraints excluded: chain D residue 88 SER 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 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: 2.9990 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 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 = 0.4142 r_free = 0.4142 target = 0.108388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.090447 restraints weight = 71728.930| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.39 r_work: 0.3633 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 8422 Z= 0.285 Angle : 0.702 4.546 12124 Z= 0.432 Chirality : 0.045 0.152 1386 Planarity : 0.006 0.044 916 Dihedral : 28.573 87.979 2553 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: 0.13 (0.34), residues: 520 helix: 0.82 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -2.14 (0.46), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 30 TYR 0.026 0.002 TYR A 100 PHE 0.016 0.003 PHE A 105 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 8422) covalent geometry : angle 0.70238 (12124) hydrogen bonds : bond 0.08336 ( 496) hydrogen bonds : angle 3.99640 ( 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 124 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 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: A 80 LYS cc_start: 0.8445 (tttp) cc_final: 0.8124 (ttmt) REVERT: B 85 MET cc_start: 0.4912 (mmp) cc_final: 0.4565 (mmp) REVERT: H 93 ARG cc_start: 0.6910 (mmp80) cc_final: 0.6534 (mmp80) REVERT: H 94 GLU cc_start: 0.8258 (mp0) cc_final: 0.7691 (mm-30) outliers start: 19 outliers final: 17 residues processed: 117 average time/residue: 0.3178 time to fit residues: 43.9738 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 : 0.290 ------------------------------------------------------------------------------- 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 59 LEU 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 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 101 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 89 THR 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: 5.9990 chunk 60 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.111461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.093589 restraints weight = 70534.807| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 3.37 r_work: 0.3689 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8422 Z= 0.176 Angle : 0.620 4.559 12124 Z= 0.383 Chirality : 0.039 0.153 1386 Planarity : 0.004 0.044 916 Dihedral : 28.413 88.916 2553 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.25 % Allowed : 19.78 % 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: 1.07 (0.35), residues: 520 helix: 1.57 (0.25), residues: 391 sheet: None (None), residues: 0 loop : -2.04 (0.46), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 36 TYR 0.014 0.001 TYR A 100 PHE 0.011 0.001 PHE D 66 HIS 0.003 0.001 HIS H 83 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8422) covalent geometry : angle 0.61998 (12124) hydrogen bonds : bond 0.05456 ( 496) hydrogen bonds : angle 3.31702 ( 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 113 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.307 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: A 80 LYS cc_start: 0.8435 (tttp) cc_final: 0.8104 (ttmt) REVERT: B 85 MET cc_start: 0.4668 (mmp) cc_final: 0.4402 (mmp) REVERT: G 43 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.8187 (mtp-110) REVERT: G 74 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8091 (t0) REVERT: H 93 ARG cc_start: 0.6687 (mmp80) cc_final: 0.6362 (mmp80) REVERT: H 94 GLU cc_start: 0.8172 (mp0) cc_final: 0.7634 (mm-30) outliers start: 10 outliers final: 9 residues processed: 109 average time/residue: 0.3106 time to fit residues: 39.9544 Evaluate side-chains 109 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain D residue 88 SER 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 74 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 74 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.108524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.090229 restraints weight = 72343.608| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.49 r_work: 0.3639 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8422 Z= 0.226 Angle : 0.652 5.053 12124 Z= 0.400 Chirality : 0.041 0.153 1386 Planarity : 0.005 0.064 916 Dihedral : 28.506 89.834 2553 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.92 % Allowed : 20.45 % Favored : 76.63 % 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 (0.35), residues: 520 helix: 1.22 (0.25), residues: 391 sheet: None (None), residues: 0 loop : -2.23 (0.48), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 36 TYR 0.022 0.001 TYR A 100 PHE 0.012 0.002 PHE D 66 HIS 0.005 0.001 HIS G 32 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 8422) covalent geometry : angle 0.65230 (12124) hydrogen bonds : bond 0.07050 ( 496) hydrogen bonds : angle 3.66314 ( 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 121 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.314 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: A 80 LYS cc_start: 0.8486 (tttp) cc_final: 0.8171 (ttmt) REVERT: B 85 MET cc_start: 0.5217 (mmp) cc_final: 0.4902 (mmp) REVERT: G 74 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8121 (t0) REVERT: H 93 ARG cc_start: 0.6836 (mmp80) cc_final: 0.6464 (mmp80) REVERT: H 94 GLU cc_start: 0.8302 (mp0) cc_final: 0.7698 (mm-30) outliers start: 13 outliers final: 11 residues processed: 117 average time/residue: 0.3099 time to fit residues: 42.6641 Evaluate side-chains 116 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain D residue 88 SER 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 79 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 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 = 0.4162 r_free = 0.4162 target = 0.109738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.091443 restraints weight = 72987.300| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.55 r_work: 0.3657 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.6389 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= 0.185 Angle : 0.622 5.350 12124 Z= 0.381 Chirality : 0.039 0.152 1386 Planarity : 0.004 0.047 916 Dihedral : 28.438 89.373 2553 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.70 % Allowed : 20.67 % Favored : 76.63 % 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: 0.99 (0.36), residues: 520 helix: 1.53 (0.25), residues: 391 sheet: None (None), residues: 0 loop : -2.13 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 36 TYR 0.015 0.001 TYR A 100 PHE 0.010 0.001 PHE D 66 HIS 0.002 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8422) covalent geometry : angle 0.62178 (12124) hydrogen bonds : bond 0.05724 ( 496) hydrogen bonds : angle 3.37976 ( 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 120 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.323 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: A 80 LYS cc_start: 0.8475 (tttp) cc_final: 0.8242 (ttmt) REVERT: B 85 MET cc_start: 0.5114 (mmp) cc_final: 0.4887 (mmp) REVERT: G 74 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8096 (t0) REVERT: H 93 ARG cc_start: 0.6740 (mmp80) cc_final: 0.6383 (mmp80) REVERT: H 94 GLU cc_start: 0.8253 (mp0) cc_final: 0.7658 (mm-30) outliers start: 12 outliers final: 11 residues processed: 116 average time/residue: 0.3136 time to fit residues: 42.9202 Evaluate side-chains 118 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain D residue 88 SER 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 74 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 79 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 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 = 0.4166 r_free = 0.4166 target = 0.109968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.091924 restraints weight = 72819.442| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.53 r_work: 0.3662 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8422 Z= 0.182 Angle : 0.614 5.573 12124 Z= 0.376 Chirality : 0.039 0.139 1386 Planarity : 0.004 0.052 916 Dihedral : 28.380 89.612 2553 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.47 % Allowed : 21.57 % Favored : 75.96 % 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 (0.36), residues: 520 helix: 1.72 (0.25), residues: 391 sheet: None (None), residues: 0 loop : -2.08 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 79 TYR 0.016 0.001 TYR A 100 PHE 0.009 0.001 PHE D 66 HIS 0.002 0.001 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8422) covalent geometry : angle 0.61353 (12124) hydrogen bonds : bond 0.05550 ( 496) hydrogen bonds : angle 3.31932 ( 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 119 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8523 (tttp) cc_final: 0.8254 (ttmt) REVERT: B 85 MET cc_start: 0.5192 (mmp) cc_final: 0.4901 (mmp) REVERT: G 74 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8066 (t0) REVERT: G 92 GLU cc_start: 0.8781 (pm20) cc_final: 0.8501 (pm20) REVERT: G 95 ASN cc_start: 0.8827 (t0) cc_final: 0.8259 (m-40) REVERT: H 93 ARG cc_start: 0.6701 (mmp80) cc_final: 0.6444 (mmp80) REVERT: H 94 GLU cc_start: 0.8220 (mp0) cc_final: 0.7622 (mm-30) outliers start: 11 outliers final: 10 residues processed: 115 average time/residue: 0.3512 time to fit residues: 47.4703 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 : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain D residue 88 SER 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 74 ASN Chi-restraints excluded: chain H residue 79 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4199 r_free = 0.4199 target = 0.111349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.093870 restraints weight = 71128.357| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.25 r_work: 0.3703 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.6665 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= 0.160 Angle : 0.598 4.866 12124 Z= 0.366 Chirality : 0.037 0.135 1386 Planarity : 0.004 0.055 916 Dihedral : 28.245 89.923 2553 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.02 % Allowed : 21.80 % Favored : 76.18 % 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: 1.61 (0.37), residues: 520 helix: 2.02 (0.25), residues: 391 sheet: None (None), residues: 0 loop : -2.06 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 68 TYR 0.016 0.001 TYR H 84 PHE 0.009 0.001 PHE D 66 HIS 0.002 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8422) covalent geometry : angle 0.59815 (12124) hydrogen bonds : bond 0.04713 ( 496) hydrogen bonds : angle 3.09699 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3409.16 seconds wall clock time: 58 minutes 24.31 seconds (3504.31 seconds total)