Starting phenix.real_space_refine on Wed Aug 5 14:09:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcd_36158/08_2026/8jcd_36158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcd_36158/08_2026/8jcd_36158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jcd_36158/08_2026/8jcd_36158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcd_36158/08_2026/8jcd_36158.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcd_36158/08_2026/8jcd_36158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcd_36158/08_2026/8jcd_36158.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 240 5.49 5 S 16 5.16 5 C 5838 2.51 5 N 1986 2.21 5 O 2426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10506 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 645 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "E" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 752 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "H" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 717 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "I" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2476 Classifications: {'DNA': 120} Link IDs: {'rna3p': 119} Chain: "J" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2444 Classifications: {'DNA': 120} Link IDs: {'rna3p': 119} Time building chain proxies: 1.89, per 1000 atoms: 0.18 Number of scatterers: 10506 At special positions: 0 Unit cell: (81.62, 114.48, 115.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 240 15.00 O 2426 8.00 N 1986 7.00 C 5838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 194.2 milliseconds 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1308 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 75.7% alpha, 2.8% beta 119 base pairs and 197 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.610A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.545A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.707A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.667A pdb=" N ALA C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 59 through 69 removed outlier: 4.013A pdb=" N ARG D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL D 65 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 106 removed outlier: 3.885A pdb=" N SER D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 124 through 149 removed outlier: 3.521A pdb=" N LYS D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LEU D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN D 149 " --> pdb=" O TYR D 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.692A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.643A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.270A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.696A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 76 through 105 Processing helix chain 'H' and resid 111 through 123 Processing helix chain 'H' and resid 125 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.994A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.645A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.255A pdb=" N ARG C 42 " --> pdb=" O ILE D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.749A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.906A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.623A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.342A pdb=" N ARG G 42 " --> pdb=" O ILE H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 384 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 620 hydrogen bond angles 0 basepair planarities 119 basepair parallelities 197 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2044 1.33 - 1.45: 3571 1.45 - 1.57: 5047 1.57 - 1.69: 478 1.69 - 1.81: 28 Bond restraints: 11168 Sorted by residual: bond pdb=" C3' DG J -7 " pdb=" C2' DG J -7 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 bond pdb=" C3' DC J 4 " pdb=" C2' DC J 4 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DC I 60 " pdb=" C2' DC I 60 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DT I -50 " pdb=" C2' DT I -50 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DC J 44 " pdb=" C2' DC J 44 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 ... (remaining 11163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 15643 2.16 - 4.31: 447 4.31 - 6.47: 8 6.47 - 8.62: 2 8.62 - 10.78: 2 Bond angle restraints: 16102 Sorted by residual: angle pdb=" N3 DT J -26 " pdb=" C4 DT J -26 " pdb=" O4 DT J -26 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 16097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 4847 35.77 - 71.55: 1221 71.55 - 107.32: 12 107.32 - 143.10: 1 143.10 - 178.87: 1 Dihedral angle restraints: 6082 sinusoidal: 4056 harmonic: 2026 Sorted by residual: dihedral pdb=" CA ALA C 60 " pdb=" C ALA C 60 " pdb=" N GLU C 61 " pdb=" CA GLU C 61 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DT I -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.87 -178.87 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 4 " pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " pdb=" P DC J 5 " ideal model delta sinusoidal sigma weight residual 220.00 88.26 131.74 1 3.50e+01 8.16e-04 1.31e+01 ... (remaining 6079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1330 0.045 - 0.090: 417 0.090 - 0.135: 88 0.135 - 0.180: 5 0.180 - 0.225: 2 Chirality restraints: 1842 Sorted by residual: chirality pdb=" CG LEU G 63 " pdb=" CB LEU G 63 " pdb=" CD1 LEU G 63 " pdb=" CD2 LEU G 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CG LEU H 121 " pdb=" CB LEU H 121 " pdb=" CD1 LEU H 121 " pdb=" CD2 LEU H 121 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' DT I -17 " pdb=" C4' DT I -17 " pdb=" O3' DT I -17 " pdb=" C2' DT I -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 1839 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " 0.023 2.00e-02 2.50e+03 1.01e-02 2.83e+00 pdb=" N9 DA I 26 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO C 80 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 61 " 0.009 2.00e-02 2.50e+03 1.08e-02 2.34e+00 pdb=" CG TYR D 61 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR D 61 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 61 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 61 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 61 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 61 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 61 " -0.001 2.00e-02 2.50e+03 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1121 2.75 - 3.29: 9702 3.29 - 3.82: 20983 3.82 - 4.36: 23281 4.36 - 4.90: 34800 Nonbonded interactions: 89887 Sorted by model distance: nonbonded pdb=" OD2 ASP D 89 " pdb=" OH TYR F 98 " model vdw 2.208 3.040 nonbonded pdb=" O ILE G 78 " pdb=" OG SER H 76 " model vdw 2.215 3.040 nonbonded pdb=" N2 DG I 18 " pdb=" O2 DT J -17 " model vdw 2.225 3.120 nonbonded pdb=" O LEU A 61 " pdb=" NH2 ARG B 36 " model vdw 2.232 3.120 nonbonded pdb=" NE2 HIS B 75 " pdb=" OE2 GLU D 114 " model vdw 2.259 3.120 ... (remaining 89882 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 22 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 105) } ncs_group { reference = (chain 'D' and resid 57 through 146) selection = (chain 'H' and resid 57 through 146) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.790 Find NCS groups from input model: 0.100 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 11168 Z= 0.499 Angle : 0.740 10.776 16102 Z= 0.641 Chirality : 0.044 0.225 1842 Planarity : 0.004 0.042 1208 Dihedral : 28.678 178.870 4774 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 0.69 % Allowed : 35.68 % Favored : 63.64 % 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: 1.81 (0.32), residues: 688 helix: 1.93 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.28 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 92 TYR 0.026 0.001 TYR D 61 PHE 0.014 0.001 PHE C 25 TRP 0.008 0.002 TRP D 113 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.50 (11168) covalent geometry : angle 0.74042 / 0.64 (16102) hydrogen bonds : bond 0.09157 / 5.74 ( 694) hydrogen bonds : angle 3.83747 / 2.86 ( 1760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 233 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7753 (tm-30) REVERT: A 59 GLU cc_start: 0.8231 (pm20) cc_final: 0.7667 (pm20) REVERT: A 97 GLU cc_start: 0.8707 (tt0) cc_final: 0.8422 (tt0) REVERT: A 133 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8275 (tt0) REVERT: B 30 THR cc_start: 0.9113 (p) cc_final: 0.8760 (t) REVERT: B 98 TYR cc_start: 0.8755 (m-10) cc_final: 0.8487 (m-10) REVERT: C 56 GLU cc_start: 0.8844 (tt0) cc_final: 0.8495 (tt0) REVERT: C 68 ASN cc_start: 0.9424 (m-40) cc_final: 0.8403 (m-40) REVERT: C 95 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8557 (tppt) REVERT: D 78 GLU cc_start: 0.8730 (mp0) cc_final: 0.8484 (mp0) REVERT: E 133 GLU cc_start: 0.8565 (pt0) cc_final: 0.8327 (pt0) REVERT: F 25 ASN cc_start: 0.9195 (m-40) cc_final: 0.8526 (t0) REVERT: F 79 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7915 (mttt) REVERT: F 88 TYR cc_start: 0.9403 (m-80) cc_final: 0.9197 (m-80) REVERT: F 91 LYS cc_start: 0.9225 (ttpt) cc_final: 0.8965 (ttmt) REVERT: G 81 ARG cc_start: 0.8639 (tpt170) cc_final: 0.8265 (tpt170) REVERT: G 95 LYS cc_start: 0.9338 (ttmt) cc_final: 0.9073 (ttmm) REVERT: G 104 GLN cc_start: 0.8635 (mp10) cc_final: 0.8267 (mp10) REVERT: H 85 SER cc_start: 0.9249 (t) cc_final: 0.8963 (t) REVERT: H 89 ASP cc_start: 0.9030 (t70) cc_final: 0.8599 (t0) REVERT: H 92 ASP cc_start: 0.9232 (t70) cc_final: 0.8998 (t0) REVERT: H 141 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8548 (ttm110) outliers start: 4 outliers final: 1 residues processed: 234 average time/residue: 0.1260 time to fit residues: 37.8547 Evaluate side-chains 204 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS D 126 GLN E 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.085403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.059436 restraints weight = 30877.658| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.85 r_work: 0.2755 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11168 Z= 0.151 Angle : 0.637 8.112 16102 Z= 0.378 Chirality : 0.043 0.296 1842 Planarity : 0.005 0.045 1208 Dihedral : 30.599 177.383 3392 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.34 % Favored : 96.51 % Rotamer: Outliers : 3.43 % Allowed : 34.31 % Favored : 62.26 % 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: 2.01 (0.33), residues: 688 helix: 2.04 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.27 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 71 TYR 0.015 0.002 TYR D 61 PHE 0.010 0.001 PHE C 25 TRP 0.004 0.001 TRP D 113 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.15 (11168) covalent geometry : angle 0.63714 / 0.38 (16102) hydrogen bonds : bond 0.04690 / 3.17 ( 694) hydrogen bonds : angle 3.40675 / 2.51 ( 1760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7609 (tm-30) REVERT: A 59 GLU cc_start: 0.7769 (pm20) cc_final: 0.7503 (pm20) REVERT: A 60 LEU cc_start: 0.9063 (mt) cc_final: 0.8628 (mt) REVERT: A 94 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8640 (mm-30) REVERT: A 123 ASP cc_start: 0.9241 (m-30) cc_final: 0.9035 (m-30) REVERT: A 133 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8381 (tt0) REVERT: B 98 TYR cc_start: 0.8550 (m-10) cc_final: 0.8157 (m-80) REVERT: C 56 GLU cc_start: 0.8516 (tt0) cc_final: 0.8145 (tt0) REVERT: C 68 ASN cc_start: 0.8885 (m-40) cc_final: 0.8445 (m-40) REVERT: D 64 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.8229 (mtt90) REVERT: E 133 GLU cc_start: 0.8501 (pt0) cc_final: 0.8174 (pt0) REVERT: F 25 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8217 (t0) REVERT: F 50 ILE cc_start: 0.9225 (mm) cc_final: 0.9010 (mt) REVERT: F 79 LYS cc_start: 0.7792 (mtmt) cc_final: 0.7564 (mttt) REVERT: F 84 MET cc_start: 0.8589 (mpp) cc_final: 0.8195 (tpp) REVERT: F 88 TYR cc_start: 0.9083 (m-10) cc_final: 0.8836 (m-80) REVERT: F 91 LYS cc_start: 0.8982 (ttpt) cc_final: 0.8725 (ttmt) REVERT: G 81 ARG cc_start: 0.8584 (tpt170) cc_final: 0.8213 (tpt170) REVERT: G 104 GLN cc_start: 0.8613 (mp10) cc_final: 0.8270 (mp10) REVERT: H 85 SER cc_start: 0.8880 (t) cc_final: 0.8413 (t) REVERT: H 89 ASP cc_start: 0.8860 (t70) cc_final: 0.8427 (t0) REVERT: H 141 ARG cc_start: 0.8934 (mtp85) cc_final: 0.8515 (ttm110) outliers start: 20 outliers final: 7 residues processed: 228 average time/residue: 0.1216 time to fit residues: 35.8534 Evaluate side-chains 211 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 7.9990 chunk 78 optimal weight: 30.0000 chunk 69 optimal weight: 30.0000 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.084236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.057153 restraints weight = 31231.158| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.86 r_work: 0.2703 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11168 Z= 0.196 Angle : 0.653 8.282 16102 Z= 0.379 Chirality : 0.044 0.304 1842 Planarity : 0.005 0.054 1208 Dihedral : 30.779 176.527 3390 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 4.80 % Allowed : 32.59 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.33), residues: 688 helix: 2.20 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.35 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 116 TYR 0.019 0.002 TYR D 61 PHE 0.009 0.001 PHE A 67 TRP 0.003 0.001 TRP H 113 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.20 (11168) covalent geometry : angle 0.65312 / 0.38 (16102) hydrogen bonds : bond 0.04552 / 3.10 ( 694) hydrogen bonds : angle 3.37657 / 2.49 ( 1760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7546 (tm-30) REVERT: A 59 GLU cc_start: 0.7878 (pm20) cc_final: 0.7420 (pm20) REVERT: A 133 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8421 (tt0) REVERT: B 98 TYR cc_start: 0.8813 (m-10) cc_final: 0.8441 (m-80) REVERT: C 56 GLU cc_start: 0.8559 (tt0) cc_final: 0.8190 (tt0) REVERT: C 68 ASN cc_start: 0.8877 (m-40) cc_final: 0.8611 (m-40) REVERT: C 104 GLN cc_start: 0.8795 (mp10) cc_final: 0.8507 (mp10) REVERT: D 137 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8396 (mtmm) REVERT: E 129 ARG cc_start: 0.9166 (ttm-80) cc_final: 0.8717 (tpt90) REVERT: E 133 GLU cc_start: 0.8521 (pt0) cc_final: 0.8166 (pt0) REVERT: F 25 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8258 (t0) REVERT: F 50 ILE cc_start: 0.9207 (mm) cc_final: 0.8972 (mt) REVERT: F 53 GLU cc_start: 0.8866 (tp30) cc_final: 0.8662 (tp30) REVERT: F 79 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7630 (mttt) REVERT: F 84 MET cc_start: 0.8596 (mpp) cc_final: 0.8213 (tpp) REVERT: F 88 TYR cc_start: 0.9102 (m-10) cc_final: 0.8854 (m-80) REVERT: F 91 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8857 (ttmt) REVERT: G 81 ARG cc_start: 0.8573 (tpt170) cc_final: 0.8203 (tpt170) REVERT: G 104 GLN cc_start: 0.8675 (mp10) cc_final: 0.8292 (mp10) REVERT: H 85 SER cc_start: 0.8883 (t) cc_final: 0.8467 (t) REVERT: H 89 ASP cc_start: 0.8832 (t70) cc_final: 0.8430 (t0) REVERT: H 141 ARG cc_start: 0.8939 (mtp85) cc_final: 0.8496 (ttm110) outliers start: 28 outliers final: 15 residues processed: 221 average time/residue: 0.1093 time to fit residues: 31.6020 Evaluate side-chains 209 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.084844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.057875 restraints weight = 31493.003| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.89 r_work: 0.2722 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11168 Z= 0.155 Angle : 0.630 7.976 16102 Z= 0.367 Chirality : 0.043 0.304 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.813 176.405 3390 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 3.95 % Allowed : 35.33 % Favored : 60.72 % 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: 2.34 (0.33), residues: 688 helix: 2.31 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.28 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 32 TYR 0.018 0.001 TYR D 61 PHE 0.007 0.001 PHE C 25 TRP 0.005 0.001 TRP H 113 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (11168) covalent geometry : angle 0.63001 / 0.37 (16102) hydrogen bonds : bond 0.04191 / 2.86 ( 694) hydrogen bonds : angle 3.26431 / 2.40 ( 1760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7594 (tm-30) REVERT: A 59 GLU cc_start: 0.7923 (pm20) cc_final: 0.7472 (pm20) REVERT: A 94 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8759 (mm-30) REVERT: A 133 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8412 (tt0) REVERT: B 74 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8782 (mm-30) REVERT: B 98 TYR cc_start: 0.8772 (m-10) cc_final: 0.8500 (m-10) REVERT: C 24 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8733 (mm110) REVERT: C 56 GLU cc_start: 0.8564 (tt0) cc_final: 0.8122 (tt0) REVERT: C 68 ASN cc_start: 0.8823 (m-40) cc_final: 0.8582 (m-40) REVERT: C 104 GLN cc_start: 0.8820 (mp10) cc_final: 0.8421 (mp10) REVERT: D 137 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8375 (mtmm) REVERT: E 129 ARG cc_start: 0.9177 (ttm-80) cc_final: 0.8839 (tpt-90) REVERT: F 25 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8203 (t0) REVERT: F 53 GLU cc_start: 0.8861 (tp30) cc_final: 0.8646 (tp30) REVERT: F 79 LYS cc_start: 0.7828 (mtmt) cc_final: 0.7607 (mttt) REVERT: F 84 MET cc_start: 0.8619 (tpp) cc_final: 0.8251 (tpp) REVERT: F 88 TYR cc_start: 0.9087 (m-10) cc_final: 0.8856 (m-80) REVERT: F 91 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8842 (ttmt) REVERT: G 81 ARG cc_start: 0.8553 (tpt170) cc_final: 0.8215 (tpt170) REVERT: G 104 GLN cc_start: 0.8666 (mp10) cc_final: 0.8328 (mp10) REVERT: H 85 SER cc_start: 0.8829 (t) cc_final: 0.8456 (t) REVERT: H 89 ASP cc_start: 0.8818 (t70) cc_final: 0.8410 (t0) REVERT: H 116 ARG cc_start: 0.8188 (ttt90) cc_final: 0.7644 (ttt90) REVERT: H 132 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7712 (mt-10) REVERT: H 141 ARG cc_start: 0.8907 (mtp85) cc_final: 0.8453 (ttm110) outliers start: 23 outliers final: 13 residues processed: 220 average time/residue: 0.1230 time to fit residues: 35.2793 Evaluate side-chains 212 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 30.0000 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 80 optimal weight: 50.0000 chunk 7 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.084943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.057191 restraints weight = 30967.714| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.96 r_work: 0.2740 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11168 Z= 0.141 Angle : 0.615 7.863 16102 Z= 0.361 Chirality : 0.042 0.303 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.807 176.183 3390 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 4.46 % Allowed : 35.16 % Favored : 60.38 % 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: 2.45 (0.33), residues: 688 helix: 2.41 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.33 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 32 TYR 0.018 0.001 TYR D 61 PHE 0.008 0.001 PHE A 67 TRP 0.006 0.001 TRP H 113 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (11168) covalent geometry : angle 0.61460 / 0.36 (16102) hydrogen bonds : bond 0.04004 / 2.74 ( 694) hydrogen bonds : angle 3.18988 / 2.35 ( 1760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7594 (tm-30) REVERT: A 59 GLU cc_start: 0.7888 (pm20) cc_final: 0.7507 (pm20) REVERT: A 94 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8702 (mm-30) REVERT: A 133 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8379 (tt0) REVERT: B 92 ARG cc_start: 0.9139 (ttp80) cc_final: 0.8628 (mmm-85) REVERT: B 98 TYR cc_start: 0.8638 (m-10) cc_final: 0.8434 (m-80) REVERT: C 56 GLU cc_start: 0.8510 (tt0) cc_final: 0.8073 (tt0) REVERT: C 68 ASN cc_start: 0.8785 (m-40) cc_final: 0.8511 (m-40) REVERT: C 104 GLN cc_start: 0.8800 (mp10) cc_final: 0.8381 (mp10) REVERT: D 78 GLU cc_start: 0.8711 (mp0) cc_final: 0.8404 (mp0) REVERT: D 137 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8296 (mtmm) REVERT: E 129 ARG cc_start: 0.9078 (ttm-80) cc_final: 0.8600 (tpt90) REVERT: F 25 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8186 (t0) REVERT: F 53 GLU cc_start: 0.8856 (tp30) cc_final: 0.8629 (tp30) REVERT: F 79 LYS cc_start: 0.7815 (mtmt) cc_final: 0.7601 (mttt) REVERT: F 84 MET cc_start: 0.8617 (tpp) cc_final: 0.8234 (tpp) REVERT: F 88 TYR cc_start: 0.9115 (m-10) cc_final: 0.8912 (m-80) REVERT: F 91 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8777 (ttmt) REVERT: G 81 ARG cc_start: 0.8538 (tpt170) cc_final: 0.8210 (tpt170) REVERT: G 104 GLN cc_start: 0.8705 (mp10) cc_final: 0.8347 (mp10) REVERT: H 85 SER cc_start: 0.8785 (t) cc_final: 0.8407 (t) REVERT: H 89 ASP cc_start: 0.8844 (t70) cc_final: 0.8411 (t0) REVERT: H 116 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7562 (ttt90) REVERT: H 132 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7624 (mt-10) REVERT: H 141 ARG cc_start: 0.8902 (mtp85) cc_final: 0.8465 (ttm110) outliers start: 26 outliers final: 13 residues processed: 222 average time/residue: 0.1130 time to fit residues: 32.8431 Evaluate side-chains 209 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.085190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.057428 restraints weight = 31089.592| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.95 r_work: 0.2751 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11168 Z= 0.139 Angle : 0.619 8.616 16102 Z= 0.361 Chirality : 0.042 0.304 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.813 175.877 3390 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.91 % Favored : 96.95 % Rotamer: Outliers : 4.29 % Allowed : 34.31 % Favored : 61.41 % 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: 2.54 (0.33), residues: 688 helix: 2.46 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.27 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 92 TYR 0.020 0.001 TYR D 61 PHE 0.015 0.001 PHE C 25 TRP 0.006 0.001 TRP H 113 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (11168) covalent geometry : angle 0.61922 / 0.36 (16102) hydrogen bonds : bond 0.03936 / 2.70 ( 694) hydrogen bonds : angle 3.14887 / 2.32 ( 1760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7611 (tm-30) REVERT: A 59 GLU cc_start: 0.7947 (pm20) cc_final: 0.7562 (pm20) REVERT: A 94 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8689 (mm-30) REVERT: A 133 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8383 (tt0) REVERT: B 92 ARG cc_start: 0.9153 (ttp80) cc_final: 0.8636 (mmm-85) REVERT: B 98 TYR cc_start: 0.8633 (m-10) cc_final: 0.8421 (m-80) REVERT: C 25 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: C 56 GLU cc_start: 0.8536 (tt0) cc_final: 0.7989 (tt0) REVERT: C 68 ASN cc_start: 0.8780 (m-40) cc_final: 0.8505 (m-40) REVERT: C 104 GLN cc_start: 0.8840 (mp10) cc_final: 0.8429 (mp10) REVERT: D 137 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8249 (mtmm) REVERT: E 129 ARG cc_start: 0.9092 (ttm-80) cc_final: 0.8658 (tpt90) REVERT: E 133 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: F 25 ASN cc_start: 0.8989 (m-40) cc_final: 0.8196 (t0) REVERT: F 53 GLU cc_start: 0.8868 (tp30) cc_final: 0.8445 (tp30) REVERT: F 79 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7629 (mttt) REVERT: F 84 MET cc_start: 0.8614 (tpp) cc_final: 0.8233 (tpp) REVERT: F 88 TYR cc_start: 0.9125 (m-10) cc_final: 0.8922 (m-80) REVERT: F 91 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8758 (ttmt) REVERT: G 81 ARG cc_start: 0.8572 (tpt170) cc_final: 0.8259 (tpt170) REVERT: G 104 GLN cc_start: 0.8745 (mp10) cc_final: 0.8383 (mp10) REVERT: H 85 SER cc_start: 0.8789 (t) cc_final: 0.8449 (t) REVERT: H 89 ASP cc_start: 0.8856 (t70) cc_final: 0.8435 (t0) REVERT: H 116 ARG cc_start: 0.8226 (ttt90) cc_final: 0.7583 (ttt90) REVERT: H 132 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7567 (mt-10) REVERT: H 141 ARG cc_start: 0.8912 (mtp85) cc_final: 0.8478 (ttm110) outliers start: 25 outliers final: 17 residues processed: 218 average time/residue: 0.1163 time to fit residues: 33.3128 Evaluate side-chains 215 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 20.0000 chunk 91 optimal weight: 50.0000 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 50.0000 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.080786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.052845 restraints weight = 31185.547| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.92 r_work: 0.2625 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 11168 Z= 0.338 Angle : 0.791 10.209 16102 Z= 0.433 Chirality : 0.049 0.335 1842 Planarity : 0.005 0.047 1208 Dihedral : 31.163 174.536 3390 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 5.32 % Allowed : 34.99 % Favored : 59.69 % 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 (0.32), residues: 688 helix: 2.12 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.47 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 92 TYR 0.028 0.002 TYR D 61 PHE 0.017 0.002 PHE E 84 TRP 0.006 0.002 TRP H 113 HIS 0.006 0.002 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.34 (11168) covalent geometry : angle 0.79149 / 0.43 (16102) hydrogen bonds : bond 0.05467 / 3.72 ( 694) hydrogen bonds : angle 3.67708 / 2.70 ( 1760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7522 (tm-30) REVERT: A 59 GLU cc_start: 0.8014 (pm20) cc_final: 0.7547 (pm20) REVERT: A 133 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8477 (tt0) REVERT: B 23 ARG cc_start: 0.9066 (tpp80) cc_final: 0.8705 (mmp80) REVERT: B 46 ILE cc_start: 0.9209 (mt) cc_final: 0.9001 (mm) REVERT: B 95 ARG cc_start: 0.8655 (ttm-80) cc_final: 0.8386 (ttm110) REVERT: C 56 GLU cc_start: 0.8711 (tt0) cc_final: 0.8308 (tt0) REVERT: C 68 ASN cc_start: 0.8843 (m-40) cc_final: 0.8616 (m-40) REVERT: C 104 GLN cc_start: 0.8852 (mp10) cc_final: 0.8318 (mp10) REVERT: D 129 LYS cc_start: 0.7875 (pttm) cc_final: 0.7614 (mmmm) REVERT: D 137 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8371 (mtmm) REVERT: E 129 ARG cc_start: 0.9098 (ttm-80) cc_final: 0.8644 (tpt90) REVERT: E 133 GLU cc_start: 0.8598 (pt0) cc_final: 0.7649 (pm20) REVERT: F 25 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8283 (t0) REVERT: F 53 GLU cc_start: 0.9011 (tp30) cc_final: 0.8581 (tp30) REVERT: F 84 MET cc_start: 0.8573 (tpp) cc_final: 0.8220 (tpp) REVERT: F 88 TYR cc_start: 0.9123 (m-80) cc_final: 0.8884 (m-80) REVERT: F 91 LYS cc_start: 0.9128 (ttpt) cc_final: 0.8914 (ttmt) REVERT: G 35 ARG cc_start: 0.9233 (mtm110) cc_final: 0.8809 (ttm-80) REVERT: G 81 ARG cc_start: 0.8735 (tpt170) cc_final: 0.8361 (tpt170) REVERT: G 104 GLN cc_start: 0.8932 (mp10) cc_final: 0.8576 (mp10) REVERT: H 85 SER cc_start: 0.9037 (t) cc_final: 0.8673 (t) REVERT: H 89 ASP cc_start: 0.8836 (t70) cc_final: 0.8485 (t0) REVERT: H 141 ARG cc_start: 0.8909 (mtp85) cc_final: 0.8478 (ttm110) outliers start: 31 outliers final: 23 residues processed: 208 average time/residue: 0.1419 time to fit residues: 37.8009 Evaluate side-chains 207 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 50.0000 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.083575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.056011 restraints weight = 30735.849| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.91 r_work: 0.2712 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11168 Z= 0.144 Angle : 0.650 10.138 16102 Z= 0.374 Chirality : 0.043 0.308 1842 Planarity : 0.005 0.045 1208 Dihedral : 31.064 175.003 3390 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 3.09 % Allowed : 37.39 % Favored : 59.52 % 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: 2.40 (0.33), residues: 688 helix: 2.36 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.29 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.023 0.002 TYR D 145 PHE 0.012 0.001 PHE C 25 TRP 0.007 0.002 TRP D 113 HIS 0.002 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (11168) covalent geometry : angle 0.64968 / 0.37 (16102) hydrogen bonds : bond 0.03905 / 2.66 ( 694) hydrogen bonds : angle 3.20741 / 2.36 ( 1760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7606 (tm-30) REVERT: A 59 GLU cc_start: 0.8104 (pm20) cc_final: 0.7634 (pm20) REVERT: A 133 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8366 (tt0) REVERT: B 74 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8915 (mm-30) REVERT: C 56 GLU cc_start: 0.8636 (tt0) cc_final: 0.8169 (tt0) REVERT: C 68 ASN cc_start: 0.8748 (m-40) cc_final: 0.8536 (m-40) REVERT: C 104 GLN cc_start: 0.8891 (mp10) cc_final: 0.8364 (mp10) REVERT: D 137 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8325 (mtmm) REVERT: E 129 ARG cc_start: 0.9092 (ttm-80) cc_final: 0.8627 (tpt90) REVERT: E 133 GLU cc_start: 0.8683 (pt0) cc_final: 0.7697 (pm20) REVERT: F 25 ASN cc_start: 0.9015 (m-40) cc_final: 0.8162 (t0) REVERT: F 53 GLU cc_start: 0.8929 (tp30) cc_final: 0.8670 (tp30) REVERT: F 84 MET cc_start: 0.8575 (tpp) cc_final: 0.8181 (tpp) REVERT: F 88 TYR cc_start: 0.9135 (m-10) cc_final: 0.8916 (m-80) REVERT: G 35 ARG cc_start: 0.9207 (mtm110) cc_final: 0.8845 (ttm-80) REVERT: G 50 TYR cc_start: 0.8884 (t80) cc_final: 0.8100 (t80) REVERT: G 81 ARG cc_start: 0.8574 (tpt170) cc_final: 0.8248 (tpt170) REVERT: G 92 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8737 (mm-30) REVERT: G 104 GLN cc_start: 0.8901 (mp10) cc_final: 0.8537 (mp10) REVERT: H 141 ARG cc_start: 0.8908 (mtp85) cc_final: 0.8426 (ttm110) outliers start: 18 outliers final: 14 residues processed: 211 average time/residue: 0.1238 time to fit residues: 33.6710 Evaluate side-chains 203 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 104 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 81 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 50.0000 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.082857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.054896 restraints weight = 30849.393| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.91 r_work: 0.2737 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11168 Z= 0.185 Angle : 0.682 9.740 16102 Z= 0.385 Chirality : 0.044 0.341 1842 Planarity : 0.005 0.045 1208 Dihedral : 31.052 174.696 3390 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 2.92 % Allowed : 37.91 % Favored : 59.18 % 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: 2.41 (0.33), residues: 688 helix: 2.36 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.25 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 35 TYR 0.023 0.002 TYR D 61 PHE 0.013 0.001 PHE C 25 TRP 0.004 0.001 TRP D 113 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (11168) covalent geometry : angle 0.68174 / 0.39 (16102) hydrogen bonds : bond 0.04059 / 2.79 ( 694) hydrogen bonds : angle 3.26967 / 2.40 ( 1760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7640 (tm-30) REVERT: A 59 GLU cc_start: 0.8171 (pm20) cc_final: 0.7733 (pm20) REVERT: A 133 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8400 (tt0) REVERT: B 74 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8950 (mm-30) REVERT: C 56 GLU cc_start: 0.8688 (tt0) cc_final: 0.8218 (tt0) REVERT: C 68 ASN cc_start: 0.8785 (m-40) cc_final: 0.8562 (m-40) REVERT: C 104 GLN cc_start: 0.8929 (mp10) cc_final: 0.8392 (mp10) REVERT: D 137 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8315 (mtmm) REVERT: E 129 ARG cc_start: 0.9135 (ttm-80) cc_final: 0.8682 (tpt90) REVERT: E 133 GLU cc_start: 0.8727 (pt0) cc_final: 0.7761 (pm20) REVERT: F 25 ASN cc_start: 0.9065 (m-40) cc_final: 0.8244 (t0) REVERT: F 53 GLU cc_start: 0.8970 (tp30) cc_final: 0.8532 (tp30) REVERT: F 84 MET cc_start: 0.8612 (tpp) cc_final: 0.8234 (tpp) REVERT: G 35 ARG cc_start: 0.9244 (mtm110) cc_final: 0.8855 (ttm-80) REVERT: G 81 ARG cc_start: 0.8675 (tpt170) cc_final: 0.8349 (tpt170) REVERT: G 104 GLN cc_start: 0.8926 (mp10) cc_final: 0.8546 (mp10) REVERT: H 141 ARG cc_start: 0.8936 (mtp85) cc_final: 0.8475 (ttm110) outliers start: 17 outliers final: 15 residues processed: 202 average time/residue: 0.1255 time to fit residues: 33.0398 Evaluate side-chains 203 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 104 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.084700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.057455 restraints weight = 30805.213| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.89 r_work: 0.2740 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 11168 Z= 0.145 Angle : 0.664 10.002 16102 Z= 0.379 Chirality : 0.043 0.337 1842 Planarity : 0.005 0.072 1208 Dihedral : 30.996 174.874 3390 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 2.92 % Allowed : 37.91 % Favored : 59.18 % 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: 2.39 (0.32), residues: 688 helix: 2.33 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.23 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 103 TYR 0.021 0.002 TYR D 61 PHE 0.012 0.001 PHE C 25 TRP 0.009 0.001 TRP D 113 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (11168) covalent geometry : angle 0.66352 / 0.38 (16102) hydrogen bonds : bond 0.03834 / 2.62 ( 694) hydrogen bonds : angle 3.17445 / 2.33 ( 1760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7655 (tm-30) REVERT: A 59 GLU cc_start: 0.8156 (pm20) cc_final: 0.7709 (pm20) REVERT: A 133 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8372 (tt0) REVERT: B 74 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8950 (mm-30) REVERT: C 56 GLU cc_start: 0.8593 (tt0) cc_final: 0.8169 (tt0) REVERT: C 104 GLN cc_start: 0.8929 (mp10) cc_final: 0.8397 (mp10) REVERT: D 137 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8377 (mtmm) REVERT: E 129 ARG cc_start: 0.9083 (ttm-80) cc_final: 0.8641 (tpt90) REVERT: E 133 GLU cc_start: 0.8715 (pt0) cc_final: 0.7772 (pm20) REVERT: F 25 ASN cc_start: 0.9021 (m-40) cc_final: 0.8133 (t0) REVERT: F 53 GLU cc_start: 0.8935 (tp30) cc_final: 0.8521 (tp30) REVERT: F 84 MET cc_start: 0.8555 (tpp) cc_final: 0.8277 (tpp) REVERT: G 35 ARG cc_start: 0.9217 (mtm110) cc_final: 0.8885 (ttm-80) REVERT: G 41 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8753 (pt0) REVERT: G 71 ARG cc_start: 0.9093 (mmm-85) cc_final: 0.8845 (mmm-85) REVERT: G 81 ARG cc_start: 0.8589 (tpt170) cc_final: 0.8274 (tpt170) REVERT: G 92 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8724 (mm-30) REVERT: G 104 GLN cc_start: 0.8843 (mp10) cc_final: 0.8462 (mp10) REVERT: H 132 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7752 (tp30) REVERT: H 141 ARG cc_start: 0.8893 (mtp85) cc_final: 0.8426 (ttm110) outliers start: 17 outliers final: 12 residues processed: 205 average time/residue: 0.1159 time to fit residues: 30.8075 Evaluate side-chains 202 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 104 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.0010 chunk 65 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 30.0000 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 90 optimal weight: 30.0000 chunk 20 optimal weight: 0.6980 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.084954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057755 restraints weight = 31008.141| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.89 r_work: 0.2750 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 11168 Z= 0.148 Angle : 0.668 11.510 16102 Z= 0.379 Chirality : 0.043 0.356 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.979 174.464 3390 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.91 % Favored : 96.95 % Rotamer: Outliers : 2.40 % Allowed : 38.42 % Favored : 59.18 % 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: 2.41 (0.32), residues: 688 helix: 2.37 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.27 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 107 TYR 0.016 0.002 TYR G 50 PHE 0.012 0.001 PHE C 25 TRP 0.007 0.001 TRP D 113 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (11168) covalent geometry : angle 0.66801 / 0.38 (16102) hydrogen bonds : bond 0.03834 / 2.63 ( 694) hydrogen bonds : angle 3.16600 / 2.33 ( 1760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2183.40 seconds wall clock time: 37 minutes 51.31 seconds (2271.31 seconds total)