Starting phenix.real_space_refine on Thu Jul 2 20:37:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcd_36158/07_2026/8jcd_36158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcd_36158/07_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_36158/07_2026/8jcd_36158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcd_36158/07_2026/8jcd_36158.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcd_36158/07_2026/8jcd_36158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcd_36158/07_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-dev-6108/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: 1.81, per 1000 atoms: 0.17 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: 0.72 Conformation dependent library (CDL) restraints added in 193.3 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: 1.07 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: 1.25 Time building geometry restraints manager: 0.94 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: 15646 2.16 - 4.31: 444 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: 0.470 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.500 ------------------------------------------------------------------------------- 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 : 0.733 10.776 16102 Z= 0.635 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 0.73323 / 0.63 (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 : 0.188 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: 0.1199 time to fit residues: 36.1133 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 : 0.173 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.085713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.059294 restraints weight = 31124.966| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.88 r_work: 0.2748 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1167 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= 0.149 Angle : 0.628 7.753 16102 Z= 0.374 Chirality : 0.043 0.277 1842 Planarity : 0.005 0.045 1208 Dihedral : 30.673 176.996 3392 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.34 % Favored : 96.51 % Rotamer: Outliers : 3.60 % Allowed : 33.45 % Favored : 62.95 % 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: 2.00 (0.33), residues: 688 helix: 2.04 (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 0.007 0.001 ARG G 88 TYR 0.016 0.002 TYR D 61 PHE 0.010 0.001 PHE C 25 TRP 0.005 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 0.62827 / 0.37 (16102) hydrogen bonds : bond 0.04614 / 3.14 ( 694) hydrogen bonds : angle 3.38990 / 2.50 ( 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 236 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7596 (tm-30) REVERT: A 59 GLU cc_start: 0.7740 (pm20) cc_final: 0.7476 (pm20) REVERT: A 60 LEU cc_start: 0.9058 (mt) cc_final: 0.8645 (mt) REVERT: A 94 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8640 (mm-30) REVERT: A 123 ASP cc_start: 0.9246 (m-30) cc_final: 0.9028 (m-30) REVERT: A 133 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8379 (tt0) REVERT: B 98 TYR cc_start: 0.8508 (m-10) cc_final: 0.8116 (m-80) REVERT: C 56 GLU cc_start: 0.8521 (tt0) cc_final: 0.8153 (tt0) REVERT: C 68 ASN cc_start: 0.8914 (m-40) cc_final: 0.8471 (m-40) REVERT: E 133 GLU cc_start: 0.8493 (pt0) cc_final: 0.8167 (pt0) REVERT: F 25 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8192 (t0) REVERT: F 50 ILE cc_start: 0.9226 (mm) cc_final: 0.9008 (mt) REVERT: F 84 MET cc_start: 0.8582 (mpp) cc_final: 0.8189 (tpp) REVERT: F 88 TYR cc_start: 0.9066 (m-10) cc_final: 0.8821 (m-80) REVERT: F 91 LYS cc_start: 0.8968 (ttpt) cc_final: 0.8723 (ttmt) REVERT: G 81 ARG cc_start: 0.8587 (tpt170) cc_final: 0.8232 (tpt170) REVERT: G 104 GLN cc_start: 0.8610 (mp10) cc_final: 0.8269 (mp10) REVERT: H 85 SER cc_start: 0.8849 (t) cc_final: 0.8376 (t) REVERT: H 89 ASP cc_start: 0.8854 (t70) cc_final: 0.8411 (t0) REVERT: H 141 ARG cc_start: 0.8950 (mtp85) cc_final: 0.8535 (ttm110) outliers start: 21 outliers final: 7 residues processed: 229 average time/residue: 0.1233 time to fit residues: 36.3803 Evaluate side-chains 209 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 201 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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: 8.9990 chunk 78 optimal weight: 20.0000 chunk 69 optimal weight: 30.0000 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.082524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.056112 restraints weight = 31220.218| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.86 r_work: 0.2668 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11168 Z= 0.256 Angle : 0.689 8.189 16102 Z= 0.396 Chirality : 0.045 0.291 1842 Planarity : 0.005 0.045 1208 Dihedral : 30.961 175.490 3390 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.63 % Favored : 96.22 % Rotamer: Outliers : 5.83 % Allowed : 32.93 % Favored : 61.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.32), residues: 688 helix: 2.13 (0.23), residues: 537 sheet: None (None), residues: 0 loop : -1.46 (0.46), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 32 TYR 0.024 0.002 TYR D 61 PHE 0.010 0.002 PHE A 67 TRP 0.002 0.001 TRP D 113 HIS 0.004 0.001 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.26 (11168) covalent geometry : angle 0.68939 / 0.40 (16102) hydrogen bonds : bond 0.04983 / 3.39 ( 694) hydrogen bonds : angle 3.51482 / 2.59 ( 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 226 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7514 (tm-30) REVERT: A 59 GLU cc_start: 0.7882 (pm20) cc_final: 0.7458 (pm20) REVERT: A 133 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8446 (tt0) REVERT: B 98 TYR cc_start: 0.9087 (m-10) cc_final: 0.8762 (m-80) REVERT: C 56 GLU cc_start: 0.8617 (tt0) cc_final: 0.8270 (tt0) REVERT: C 68 ASN cc_start: 0.8926 (m-40) cc_final: 0.8653 (m-40) REVERT: D 129 LYS cc_start: 0.7851 (pttm) cc_final: 0.7649 (mmmm) REVERT: D 137 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8407 (mtmm) REVERT: E 129 ARG cc_start: 0.9134 (ttm-80) cc_final: 0.8686 (tpt90) REVERT: E 133 GLU cc_start: 0.8496 (pt0) cc_final: 0.8284 (pt0) REVERT: F 25 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8225 (t0) REVERT: F 50 ILE cc_start: 0.9198 (mm) cc_final: 0.8972 (mt) REVERT: F 53 GLU cc_start: 0.8919 (tp30) cc_final: 0.8718 (tp30) REVERT: F 84 MET cc_start: 0.8547 (tpp) cc_final: 0.8170 (tpp) REVERT: F 88 TYR cc_start: 0.9072 (m-80) cc_final: 0.8835 (m-80) REVERT: F 91 LYS cc_start: 0.9095 (ttpt) cc_final: 0.8880 (ttmt) REVERT: G 81 ARG cc_start: 0.8567 (tpt170) cc_final: 0.8183 (tpt170) REVERT: G 104 GLN cc_start: 0.8665 (mp10) cc_final: 0.8298 (mp10) REVERT: H 85 SER cc_start: 0.8953 (t) cc_final: 0.8566 (t) REVERT: H 89 ASP cc_start: 0.8825 (t70) cc_final: 0.8437 (t0) REVERT: H 141 ARG cc_start: 0.8937 (mtp85) cc_final: 0.8496 (ttm110) outliers start: 34 outliers final: 17 residues processed: 217 average time/residue: 0.1183 time to fit residues: 33.7372 Evaluate side-chains 201 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 19 SER 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 E residue 112 ILE 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 74 SER 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: 6.9990 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.083794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.056044 restraints weight = 31090.715| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.95 r_work: 0.2703 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11168 Z= 0.155 Angle : 0.623 8.249 16102 Z= 0.366 Chirality : 0.042 0.285 1842 Planarity : 0.004 0.045 1208 Dihedral : 30.970 175.426 3390 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.91 % Favored : 96.95 % Rotamer: Outliers : 3.43 % Allowed : 35.16 % 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: 2.37 (0.33), residues: 688 helix: 2.35 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.37 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 116 TYR 0.024 0.002 TYR D 145 PHE 0.009 0.001 PHE C 25 TRP 0.005 0.001 TRP H 113 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.16 (11168) covalent geometry : angle 0.62307 / 0.37 (16102) hydrogen bonds : bond 0.04134 / 2.82 ( 694) hydrogen bonds : angle 3.27110 / 2.41 ( 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 224 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7600 (tm-30) REVERT: A 59 GLU cc_start: 0.7943 (pm20) cc_final: 0.7476 (pm20) REVERT: A 94 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8749 (mm-30) REVERT: A 133 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8411 (tt0) REVERT: B 46 ILE cc_start: 0.9173 (mt) cc_final: 0.8966 (mm) REVERT: B 74 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8779 (mm-30) REVERT: B 98 TYR cc_start: 0.8779 (m-10) cc_final: 0.8535 (m-80) REVERT: C 56 GLU cc_start: 0.8578 (tt0) cc_final: 0.8137 (tt0) REVERT: C 68 ASN cc_start: 0.8821 (m-40) cc_final: 0.8497 (m-40) REVERT: D 137 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8370 (mtmm) REVERT: E 129 ARG cc_start: 0.9110 (ttm-80) cc_final: 0.8622 (tpt90) REVERT: F 25 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8167 (t0) REVERT: F 53 GLU cc_start: 0.8893 (tp30) cc_final: 0.8658 (tp30) REVERT: F 84 MET cc_start: 0.8604 (tpp) cc_final: 0.8236 (tpp) REVERT: F 88 TYR cc_start: 0.9074 (m-10) cc_final: 0.8850 (m-80) REVERT: F 91 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8863 (ttmt) REVERT: G 81 ARG cc_start: 0.8538 (tpt170) cc_final: 0.8211 (tpt170) REVERT: G 104 GLN cc_start: 0.8716 (mp10) cc_final: 0.8361 (mp10) REVERT: H 83 MET cc_start: 0.8931 (tpp) cc_final: 0.8402 (tpp) REVERT: H 85 SER cc_start: 0.8820 (t) cc_final: 0.8415 (t) REVERT: H 89 ASP cc_start: 0.8806 (t70) cc_final: 0.8412 (t0) REVERT: H 116 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7693 (ttt90) REVERT: H 132 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7661 (mt-10) REVERT: H 141 ARG cc_start: 0.8910 (mtp85) cc_final: 0.8441 (ttm110) outliers start: 20 outliers final: 10 residues processed: 213 average time/residue: 0.1261 time to fit residues: 34.8788 Evaluate side-chains 206 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 101 THR 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 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=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: 1.9990 chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 0.3980 chunk 76 optimal weight: 20.0000 chunk 80 optimal weight: 50.0000 chunk 7 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.084073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.057110 restraints weight = 30711.424| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.93 r_work: 0.2728 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11168 Z= 0.148 Angle : 0.611 8.279 16102 Z= 0.361 Chirality : 0.042 0.284 1842 Planarity : 0.004 0.046 1208 Dihedral : 30.951 175.275 3390 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 4.29 % Allowed : 34.99 % 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: 2.47 (0.33), residues: 688 helix: 2.43 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.36 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 32 TYR 0.020 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 0.00264 / 0.15 (11168) covalent geometry : angle 0.61075 / 0.36 (16102) hydrogen bonds : bond 0.04039 / 2.77 ( 694) hydrogen bonds : angle 3.20616 / 2.36 ( 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 227 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7607 (tm-30) REVERT: A 59 GLU cc_start: 0.7940 (pm20) cc_final: 0.7476 (pm20) REVERT: A 94 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8702 (mm-30) REVERT: A 133 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8389 (tt0) REVERT: B 98 TYR cc_start: 0.8719 (m-10) cc_final: 0.8440 (m-10) REVERT: C 56 GLU cc_start: 0.8544 (tt0) cc_final: 0.8119 (tt0) REVERT: C 68 ASN cc_start: 0.8781 (m-40) cc_final: 0.8503 (m-40) REVERT: D 78 GLU cc_start: 0.8719 (mp0) cc_final: 0.8432 (mp0) REVERT: D 137 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8290 (mtmm) REVERT: E 129 ARG cc_start: 0.9104 (ttm-80) cc_final: 0.8619 (tpt90) REVERT: F 25 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8175 (t0) REVERT: F 53 GLU cc_start: 0.8889 (tp30) cc_final: 0.8649 (tp30) REVERT: F 84 MET cc_start: 0.8613 (tpp) cc_final: 0.8268 (tpp) REVERT: G 81 ARG cc_start: 0.8541 (tpt170) cc_final: 0.8221 (tpt170) REVERT: G 104 GLN cc_start: 0.8718 (mp10) cc_final: 0.8354 (mp10) REVERT: H 83 MET cc_start: 0.8926 (tpp) cc_final: 0.8468 (tpp) REVERT: H 85 SER cc_start: 0.8792 (t) cc_final: 0.8400 (t) REVERT: H 89 ASP cc_start: 0.8811 (t70) cc_final: 0.8374 (t0) REVERT: H 141 ARG cc_start: 0.8907 (mtp85) cc_final: 0.8438 (ttm110) outliers start: 25 outliers final: 11 residues processed: 220 average time/residue: 0.1200 time to fit residues: 34.3066 Evaluate side-chains 204 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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 H residue 75 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: 5.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.083712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055996 restraints weight = 31040.063| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.91 r_work: 0.2746 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11168 Z= 0.177 Angle : 0.639 8.546 16102 Z= 0.370 Chirality : 0.042 0.290 1842 Planarity : 0.004 0.045 1208 Dihedral : 31.006 174.741 3390 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 3.77 % Allowed : 36.88 % Favored : 59.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.33), residues: 688 helix: 2.42 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.41 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 77 TYR 0.021 0.001 TYR D 61 PHE 0.007 0.001 PHE A 67 TRP 0.005 0.001 TRP H 113 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (11168) covalent geometry : angle 0.63930 / 0.37 (16102) hydrogen bonds : bond 0.04098 / 2.81 ( 694) hydrogen bonds : angle 3.25293 / 2.39 ( 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 215 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7621 (tm-30) REVERT: A 59 GLU cc_start: 0.8107 (pm20) cc_final: 0.7627 (pm20) REVERT: A 94 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8726 (mm-30) REVERT: A 133 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8405 (tt0) REVERT: B 92 ARG cc_start: 0.9199 (ttp80) cc_final: 0.8694 (mmm-85) REVERT: B 98 TYR cc_start: 0.8857 (m-10) cc_final: 0.8613 (m-10) REVERT: C 56 GLU cc_start: 0.8656 (tt0) cc_final: 0.8191 (tt0) REVERT: C 68 ASN cc_start: 0.8808 (m-40) cc_final: 0.8489 (m-40) REVERT: D 78 GLU cc_start: 0.8799 (mp0) cc_final: 0.8485 (mp0) REVERT: D 137 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8311 (mtmm) REVERT: E 129 ARG cc_start: 0.9146 (ttm-80) cc_final: 0.8758 (tpt90) REVERT: F 25 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8234 (t0) REVERT: F 50 ILE cc_start: 0.9123 (mm) cc_final: 0.8913 (mt) REVERT: F 53 GLU cc_start: 0.8935 (tp30) cc_final: 0.8690 (tp30) REVERT: F 84 MET cc_start: 0.8627 (tpp) cc_final: 0.8345 (tpp) REVERT: G 35 ARG cc_start: 0.9242 (mtm110) cc_final: 0.8880 (ttm-80) REVERT: G 81 ARG cc_start: 0.8649 (tpt170) cc_final: 0.8341 (tpt170) REVERT: G 104 GLN cc_start: 0.8793 (mp10) cc_final: 0.8450 (mp10) REVERT: H 83 MET cc_start: 0.8990 (tpp) cc_final: 0.8507 (tpp) REVERT: H 85 SER cc_start: 0.8897 (t) cc_final: 0.8463 (t) REVERT: H 89 ASP cc_start: 0.8871 (t70) cc_final: 0.8461 (t0) REVERT: H 116 ARG cc_start: 0.8299 (ttt90) cc_final: 0.7779 (ttt90) REVERT: H 141 ARG cc_start: 0.8948 (mtp85) cc_final: 0.8505 (ttm110) outliers start: 22 outliers final: 15 residues processed: 205 average time/residue: 0.1136 time to fit residues: 30.2685 Evaluate side-chains 208 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 47 SER Chi-restraints excluded: chain C residue 27 VAL 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 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 79 ILE Chi-restraints excluded: chain H residue 74 SER 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: 40.0000 chunk 43 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 30.0000 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 0.0000 chunk 68 optimal weight: 50.0000 chunk 17 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 overall best weight: 1.9790 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.083875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.056688 restraints weight = 31257.579| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.93 r_work: 0.2712 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11168 Z= 0.166 Angle : 0.635 9.034 16102 Z= 0.369 Chirality : 0.042 0.313 1842 Planarity : 0.005 0.045 1208 Dihedral : 31.048 174.456 3390 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.91 % Favored : 96.95 % Rotamer: Outliers : 4.29 % Allowed : 37.05 % Favored : 58.66 % 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: 2.42 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.34 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 116 TYR 0.021 0.001 TYR D 61 PHE 0.007 0.001 PHE E 104 TRP 0.005 0.001 TRP H 113 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (11168) covalent geometry : angle 0.63517 / 0.37 (16102) hydrogen bonds : bond 0.03997 / 2.74 ( 694) hydrogen bonds : angle 3.22579 / 2.37 ( 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 223 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7614 (tm-30) REVERT: A 59 GLU cc_start: 0.8074 (pm20) cc_final: 0.7625 (pm20) REVERT: A 94 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8731 (mm-30) REVERT: A 133 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8416 (tt0) REVERT: B 92 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8663 (mmm-85) REVERT: B 98 TYR cc_start: 0.8827 (m-10) cc_final: 0.8575 (m-10) REVERT: C 56 GLU cc_start: 0.8603 (tt0) cc_final: 0.8136 (tt0) REVERT: C 68 ASN cc_start: 0.8784 (m-40) cc_final: 0.8552 (m-40) REVERT: C 104 GLN cc_start: 0.8753 (mp10) cc_final: 0.8521 (mp10) REVERT: D 137 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8286 (mtmm) REVERT: E 129 ARG cc_start: 0.9114 (ttm-80) cc_final: 0.8674 (tpt90) REVERT: E 133 GLU cc_start: 0.8589 (pt0) cc_final: 0.7634 (pm20) REVERT: F 25 ASN cc_start: 0.9031 (m-40) cc_final: 0.8202 (t0) REVERT: F 53 GLU cc_start: 0.8927 (tp30) cc_final: 0.8675 (tp30) REVERT: F 84 MET cc_start: 0.8595 (tpp) cc_final: 0.8323 (tpp) REVERT: G 35 ARG cc_start: 0.9223 (mtm110) cc_final: 0.8844 (ttm-80) REVERT: G 81 ARG cc_start: 0.8601 (tpt170) cc_final: 0.8295 (tpt170) REVERT: G 104 GLN cc_start: 0.8786 (mp10) cc_final: 0.8437 (mp10) REVERT: H 83 MET cc_start: 0.8977 (tpp) cc_final: 0.8598 (tpp) REVERT: H 85 SER cc_start: 0.8835 (t) cc_final: 0.8437 (t) REVERT: H 89 ASP cc_start: 0.8852 (t70) cc_final: 0.8456 (t0) REVERT: H 141 ARG cc_start: 0.8907 (mtp85) cc_final: 0.8438 (ttm110) outliers start: 25 outliers final: 18 residues processed: 216 average time/residue: 0.1149 time to fit residues: 32.0074 Evaluate side-chains 212 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 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 E residue 61 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 22 LEU 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 79 ILE 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: 0.7980 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 50.0000 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.084820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.057404 restraints weight = 30769.789| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.90 r_work: 0.2732 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11168 Z= 0.145 Angle : 0.632 9.840 16102 Z= 0.367 Chirality : 0.042 0.329 1842 Planarity : 0.005 0.076 1208 Dihedral : 31.026 174.244 3390 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.91 % Favored : 96.95 % Rotamer: Outliers : 3.26 % Allowed : 38.42 % Favored : 58.32 % 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: 2.46 (0.33), residues: 688 helix: 2.41 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 116 TYR 0.022 0.002 TYR F 88 PHE 0.007 0.001 PHE E 104 TRP 0.007 0.001 TRP H 113 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (11168) covalent geometry : angle 0.63211 / 0.37 (16102) hydrogen bonds : bond 0.03862 / 2.65 ( 694) hydrogen bonds : angle 3.15196 / 2.32 ( 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 220 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7604 (tm-30) REVERT: A 59 GLU cc_start: 0.8071 (pm20) cc_final: 0.7632 (pm20) REVERT: A 94 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8694 (mm-30) REVERT: A 133 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8403 (tt0) REVERT: B 92 ARG cc_start: 0.9137 (ttp80) cc_final: 0.8626 (mmm-85) REVERT: B 98 TYR cc_start: 0.8607 (m-10) cc_final: 0.8362 (m-10) REVERT: C 56 GLU cc_start: 0.8567 (tt0) cc_final: 0.8122 (tt0) REVERT: C 68 ASN cc_start: 0.8749 (m-40) cc_final: 0.8546 (m-40) REVERT: D 137 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8361 (mtmm) REVERT: E 129 ARG cc_start: 0.9069 (ttm-80) cc_final: 0.8603 (tpt90) REVERT: E 133 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: F 25 ASN cc_start: 0.9006 (m-40) cc_final: 0.8114 (t0) REVERT: F 53 GLU cc_start: 0.8909 (tp30) cc_final: 0.8649 (tp30) REVERT: F 84 MET cc_start: 0.8581 (tpp) cc_final: 0.8318 (tpp) REVERT: G 35 ARG cc_start: 0.9205 (mtm110) cc_final: 0.8879 (ttm-80) REVERT: G 81 ARG cc_start: 0.8559 (tpt170) cc_final: 0.8266 (tpt170) REVERT: G 92 GLU cc_start: 0.9333 (mm-30) cc_final: 0.8800 (mm-30) REVERT: G 104 GLN cc_start: 0.8796 (mp10) cc_final: 0.8443 (mp10) REVERT: H 77 ARG cc_start: 0.8630 (mtp-110) cc_final: 0.8380 (mtm110) REVERT: H 85 SER cc_start: 0.8764 (t) cc_final: 0.8333 (t) REVERT: H 89 ASP cc_start: 0.8867 (t70) cc_final: 0.8463 (t0) REVERT: H 141 ARG cc_start: 0.8868 (mtp85) cc_final: 0.8398 (ttm110) outliers start: 19 outliers final: 11 residues processed: 213 average time/residue: 0.1222 time to fit residues: 33.7064 Evaluate side-chains 206 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 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 133 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 81 optimal weight: 30.0000 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 68 optimal weight: 50.0000 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** 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 = 0.3640 r_free = 0.3640 target = 0.085220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.057809 restraints weight = 30931.440| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.95 r_work: 0.2747 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11168 Z= 0.141 Angle : 0.629 9.553 16102 Z= 0.366 Chirality : 0.042 0.326 1842 Planarity : 0.004 0.052 1208 Dihedral : 30.992 173.919 3390 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.91 % Favored : 96.95 % Rotamer: Outliers : 2.74 % Allowed : 39.11 % Favored : 58.15 % 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: 2.49 (0.33), residues: 688 helix: 2.44 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.31 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 116 TYR 0.020 0.001 TYR F 88 PHE 0.009 0.001 PHE C 25 TRP 0.007 0.001 TRP H 113 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (11168) covalent geometry : angle 0.62931 / 0.37 (16102) hydrogen bonds : bond 0.03795 / 2.61 ( 694) hydrogen bonds : angle 3.11190 / 2.30 ( 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 209 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7689 (tm-30) REVERT: A 59 GLU cc_start: 0.8091 (pm20) cc_final: 0.7653 (pm20) REVERT: A 94 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8704 (mm-30) REVERT: A 133 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8334 (tt0) REVERT: B 92 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8636 (mmm-85) REVERT: C 56 GLU cc_start: 0.8562 (tt0) cc_final: 0.8062 (tt0) REVERT: D 137 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8364 (mtmm) REVERT: E 129 ARG cc_start: 0.9056 (ttm-80) cc_final: 0.8605 (tpt90) REVERT: E 133 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: F 25 ASN cc_start: 0.9003 (m-40) cc_final: 0.8294 (t0) REVERT: F 53 GLU cc_start: 0.8914 (tp30) cc_final: 0.8478 (tp30) REVERT: F 84 MET cc_start: 0.8528 (tpp) cc_final: 0.8297 (tpp) REVERT: G 71 ARG cc_start: 0.9074 (mmm-85) cc_final: 0.8821 (mmm-85) REVERT: G 81 ARG cc_start: 0.8573 (tpt170) cc_final: 0.8286 (tpt170) REVERT: G 92 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8421 (mm-30) REVERT: G 95 LYS cc_start: 0.9284 (ttmm) cc_final: 0.8873 (ttpt) REVERT: G 104 GLN cc_start: 0.8746 (mp10) cc_final: 0.8413 (mp10) REVERT: H 77 ARG cc_start: 0.8617 (mtp-110) cc_final: 0.8054 (mtm-85) REVERT: H 85 SER cc_start: 0.8755 (t) cc_final: 0.8342 (t) REVERT: H 89 ASP cc_start: 0.8856 (t70) cc_final: 0.8435 (t0) REVERT: H 105 THR cc_start: 0.8903 (t) cc_final: 0.8652 (t) REVERT: H 141 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8432 (ttm110) outliers start: 16 outliers final: 13 residues processed: 201 average time/residue: 0.1179 time to fit residues: 30.6282 Evaluate side-chains 204 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE 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 66 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 133 GLU 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 104 SER Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.083963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.056835 restraints weight = 31046.233| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.91 r_work: 0.2720 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11168 Z= 0.182 Angle : 0.672 9.098 16102 Z= 0.382 Chirality : 0.044 0.360 1842 Planarity : 0.005 0.060 1208 Dihedral : 31.061 173.307 3390 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.49 % Favored : 96.37 % Rotamer: Outliers : 2.57 % Allowed : 38.77 % Favored : 58.66 % 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: 2.44 (0.33), residues: 688 helix: 2.41 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.34 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 116 TYR 0.023 0.002 TYR D 61 PHE 0.010 0.001 PHE C 25 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 0.00366 / 0.18 (11168) covalent geometry : angle 0.67159 / 0.38 (16102) hydrogen bonds : bond 0.04022 / 2.76 ( 694) hydrogen bonds : angle 3.23564 / 2.38 ( 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 208 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7666 (tm-30) REVERT: A 59 GLU cc_start: 0.8155 (pm20) cc_final: 0.7714 (pm20) REVERT: A 94 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8742 (mm-30) REVERT: A 133 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8394 (tt0) REVERT: C 56 GLU cc_start: 0.8616 (tt0) cc_final: 0.8136 (tt0) REVERT: D 137 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8392 (mtmm) REVERT: E 129 ARG cc_start: 0.9103 (ttm-80) cc_final: 0.8637 (tpt90) REVERT: E 133 GLU cc_start: 0.8701 (pt0) cc_final: 0.7764 (pm20) REVERT: F 25 ASN cc_start: 0.9053 (m-40) cc_final: 0.8399 (t0) REVERT: F 53 GLU cc_start: 0.8928 (tp30) cc_final: 0.8456 (tp30) REVERT: F 84 MET cc_start: 0.8551 (tpp) cc_final: 0.8329 (tpp) REVERT: G 35 ARG cc_start: 0.9233 (mtm110) cc_final: 0.8929 (ttm-80) REVERT: G 71 ARG cc_start: 0.9106 (mmm-85) cc_final: 0.8842 (mmm-85) REVERT: G 81 ARG cc_start: 0.8633 (tpt170) cc_final: 0.8324 (tpt170) REVERT: G 92 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8809 (mm-30) REVERT: G 104 GLN cc_start: 0.8759 (mp10) cc_final: 0.8427 (mp10) REVERT: H 77 ARG cc_start: 0.8651 (mtp-110) cc_final: 0.8118 (mtm-85) REVERT: H 85 SER cc_start: 0.8748 (t) cc_final: 0.8537 (t) REVERT: H 105 THR cc_start: 0.8938 (t) cc_final: 0.8727 (t) REVERT: H 126 GLN cc_start: 0.8522 (tp40) cc_final: 0.8303 (tp40) REVERT: H 141 ARG cc_start: 0.8879 (mtp85) cc_final: 0.8418 (ttm110) outliers start: 15 outliers final: 12 residues processed: 205 average time/residue: 0.1280 time to fit residues: 33.9710 Evaluate side-chains 200 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE 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 E residue 86 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 143 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 90 optimal weight: 30.0000 chunk 20 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 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 = 0.084505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.057099 restraints weight = 31073.935| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.94 r_work: 0.2738 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11168 Z= 0.151 Angle : 0.661 9.907 16102 Z= 0.378 Chirality : 0.043 0.368 1842 Planarity : 0.005 0.055 1208 Dihedral : 31.055 173.343 3390 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 2.74 % Allowed : 39.45 % Favored : 57.80 % 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: 2.49 (0.33), residues: 688 helix: 2.44 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.29 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 116 TYR 0.021 0.002 TYR D 61 PHE 0.010 0.001 PHE C 25 TRP 0.006 0.001 TRP D 113 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (11168) covalent geometry : angle 0.66141 / 0.38 (16102) hydrogen bonds : bond 0.03800 / 2.60 ( 694) hydrogen bonds : angle 3.14881 / 2.32 ( 1760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2206.99 seconds wall clock time: 38 minutes 21.60 seconds (2301.60 seconds total)