Starting phenix.real_space_refine on Wed Feb 4 14:45:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jc6_61358/02_2026/9jc6_61358.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jc6_61358/02_2026/9jc6_61358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jc6_61358/02_2026/9jc6_61358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jc6_61358/02_2026/9jc6_61358.map" model { file = "/net/cci-nas-00/data/ceres_data/9jc6_61358/02_2026/9jc6_61358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jc6_61358/02_2026/9jc6_61358.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 263 5.49 5 S 20 5.16 5 C 6321 2.51 5 N 2139 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11369 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 696 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "I" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2688 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2721 Classifications: {'DNA': 132} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 131} Time building chain proxies: 2.80, per 1000 atoms: 0.25 Number of scatterers: 11369 At special positions: 0 Unit cell: (85.86, 116.6, 116.6, 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 20 16.00 P 263 15.00 O 2626 8.00 N 2139 7.00 C 6321 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: 1.12 Conformation dependent library (CDL) restraints added in 415.3 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 71.7% alpha, 1.9% beta 133 base pairs and 221 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 23 through 29 removed outlier: 3.862A pdb=" N ILE B 26 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.514A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.527A pdb=" N LEU C 115 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.976A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 68' Processing helix chain 'D' and resid 77 through 106 removed outlier: 4.186A pdb=" N SER D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 124 removed outlier: 3.871A pdb=" N ARG D 121 " --> pdb=" O GLN D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.542A pdb=" N LEU D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 removed outlier: 3.679A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.965A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) 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: 4.107A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.553A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 62 through 69 removed outlier: 3.625A pdb=" N GLN H 69 " --> pdb=" O ARG H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 104 Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 125 through 146 removed outlier: 3.651A pdb=" N CYS H 146 " --> pdb=" O ARG H 142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 7.021A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.308A pdb=" N ARG C 42 " --> pdb=" O ILE D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 removed outlier: 3.587A pdb=" N THR C 101 " --> pdb=" O THR F 96 " (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: 6.546A 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: 3.721A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 384 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 672 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 221 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2371 1.33 - 1.45: 3697 1.45 - 1.57: 5478 1.57 - 1.69: 525 1.69 - 1.81: 34 Bond restraints: 12105 Sorted by residual: bond pdb=" CG1 ILE F 66 " pdb=" CD1 ILE F 66 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.10e+00 bond pdb=" C4' DG I 26 " pdb=" C3' DG I 26 " ideal model delta sigma weight residual 1.523 1.503 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" C4' DA I 17 " pdb=" C3' DA I 17 " ideal model delta sigma weight residual 1.523 1.504 0.019 2.00e-02 2.50e+03 9.51e-01 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.40e-01 ... (remaining 12100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 16376 1.16 - 2.32: 968 2.32 - 3.48: 107 3.48 - 4.64: 15 4.64 - 5.81: 15 Bond angle restraints: 17481 Sorted by residual: angle pdb=" N ILE E 51 " pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 111.45 109.10 2.35 9.30e-01 1.16e+00 6.37e+00 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.20e+00 angle pdb=" N GLY D 126 " pdb=" CA GLY D 126 " pdb=" C GLY D 126 " ideal model delta sigma weight residual 113.18 118.99 -5.81 2.37e+00 1.78e-01 6.00e+00 angle pdb=" CA THR D 60 " pdb=" C THR D 60 " pdb=" N PRO D 61 " ideal model delta sigma weight residual 118.44 122.18 -3.74 1.59e+00 3.96e-01 5.55e+00 angle pdb=" CA PHE B 100 " pdb=" C PHE B 100 " pdb=" O PHE B 100 " ideal model delta sigma weight residual 118.79 121.37 -2.58 1.13e+00 7.83e-01 5.22e+00 ... (remaining 17476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 5279 35.63 - 71.27: 1305 71.27 - 106.90: 21 106.90 - 142.53: 2 142.53 - 178.17: 1 Dihedral angle restraints: 6608 sinusoidal: 4437 harmonic: 2171 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.17 -178.17 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 48 " pdb=" C3' DG J 48 " pdb=" O3' DG J 48 " pdb=" P DC J 49 " ideal model delta sinusoidal sigma weight residual -140.00 -0.47 -139.53 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA ASP H 85 " pdb=" CB ASP H 85 " pdb=" CG ASP H 85 " pdb=" OD1 ASP H 85 " ideal model delta sinusoidal sigma weight residual -30.00 -88.37 58.37 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 6605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1616 0.043 - 0.085: 320 0.085 - 0.128: 54 0.128 - 0.171: 4 0.171 - 0.213: 1 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CB ILE D 111 " pdb=" CA ILE D 111 " pdb=" CG1 ILE D 111 " pdb=" CG2 ILE D 111 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" P DC J 49 " pdb=" OP1 DC J 49 " pdb=" OP2 DC J 49 " pdb=" O5' DC J 49 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 1992 not shown) Planarity restraints: 1303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I -50 " 0.005 2.00e-02 2.50e+03 1.98e-02 8.80e+00 pdb=" N1 DC I -50 " -0.014 2.00e-02 2.50e+03 pdb=" C2 DC I -50 " 0.048 2.00e-02 2.50e+03 pdb=" O2 DC I -50 " -0.029 2.00e-02 2.50e+03 pdb=" N3 DC I -50 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC I -50 " 0.008 2.00e-02 2.50e+03 pdb=" N4 DC I -50 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC I -50 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC I -50 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 51 " 0.002 2.00e-02 2.50e+03 1.15e-02 4.00e+00 pdb=" N9 DG J 51 " 0.007 2.00e-02 2.50e+03 pdb=" C8 DG J 51 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 51 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG J 51 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG J 51 " -0.009 2.00e-02 2.50e+03 pdb=" O6 DG J 51 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG J 51 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG J 51 " -0.031 2.00e-02 2.50e+03 pdb=" N2 DG J 51 " 0.020 2.00e-02 2.50e+03 pdb=" N3 DG J 51 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG J 51 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 62 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C LEU B 62 " 0.024 2.00e-02 2.50e+03 pdb=" O LEU B 62 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU B 63 " -0.008 2.00e-02 2.50e+03 ... (remaining 1300 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 5 2.25 - 2.91: 4313 2.91 - 3.57: 19938 3.57 - 4.24: 30956 4.24 - 4.90: 44296 Nonbonded interactions: 99508 Sorted by model distance: nonbonded pdb=" NE2 GLN D 101 " pdb=" OH TYR D 105 " model vdw 1.585 3.120 nonbonded pdb=" N2 DG I 71 " pdb=" O2 DC J -71 " model vdw 2.104 2.496 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR G 76 " pdb=" OP1 DG I 58 " model vdw 2.185 3.040 nonbonded pdb=" OG SER C 40 " pdb=" O VAL D 109 " model vdw 2.189 3.040 ... (remaining 99503 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 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 117) } ncs_group { reference = (chain 'D' and resid 56 through 146) selection = chain 'H' } 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: 0.660 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 13.690 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 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 : 0.004 0.052 12105 Z= 0.199 Angle : 0.604 5.805 17481 Z= 0.372 Chirality : 0.035 0.213 1995 Planarity : 0.003 0.034 1303 Dihedral : 28.617 178.165 5206 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: -2.20 (0.27), residues: 737 helix: -0.67 (0.20), residues: 504 sheet: None (None), residues: 0 loop : -3.13 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 81 TYR 0.009 0.001 TYR F 51 PHE 0.005 0.001 PHE E 104 TRP 0.002 0.001 TRP D 149 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00428 (12105) covalent geometry : angle 0.60428 (17481) hydrogen bonds : bond 0.10889 ( 724) hydrogen bonds : angle 4.48238 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9007 (pm20) cc_final: 0.8747 (pm20) REVERT: A 68 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8258 (tm-30) REVERT: A 79 LYS cc_start: 0.8553 (tttt) cc_final: 0.8341 (ttmm) REVERT: A 93 GLN cc_start: 0.9128 (tp40) cc_final: 0.8558 (tp40) REVERT: A 110 CYS cc_start: 0.8953 (t) cc_final: 0.8506 (t) REVERT: B 44 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8573 (ttmm) REVERT: B 59 LYS cc_start: 0.9182 (ttmt) cc_final: 0.8706 (tttm) REVERT: B 63 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8738 (mt-10) REVERT: B 74 GLU cc_start: 0.9253 (tp30) cc_final: 0.9031 (tp30) REVERT: C 16 THR cc_start: 0.9661 (p) cc_final: 0.9306 (p) REVERT: C 20 ARG cc_start: 0.9189 (ttm170) cc_final: 0.8674 (ttm110) REVERT: C 36 LYS cc_start: 0.9368 (tmtt) cc_final: 0.8726 (tptt) REVERT: C 56 GLU cc_start: 0.8827 (tt0) cc_final: 0.8617 (tt0) REVERT: C 57 TYR cc_start: 0.8823 (t80) cc_final: 0.8447 (t80) REVERT: C 73 ASN cc_start: 0.9642 (t0) cc_final: 0.9125 (t0) REVERT: C 75 LYS cc_start: 0.9001 (mttm) cc_final: 0.8790 (mmmm) REVERT: C 84 GLN cc_start: 0.9593 (tp40) cc_final: 0.8957 (tp40) REVERT: C 102 ILE cc_start: 0.9524 (mp) cc_final: 0.9274 (mp) REVERT: D 65 ARG cc_start: 0.8856 (ptm-80) cc_final: 0.8643 (ptp-170) REVERT: D 78 GLN cc_start: 0.9490 (tp40) cc_final: 0.9109 (tp40) REVERT: D 90 ASP cc_start: 0.9158 (t70) cc_final: 0.8953 (t0) REVERT: D 117 GLN cc_start: 0.8682 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 118 MET cc_start: 0.9390 (mmt) cc_final: 0.8824 (mmm) REVERT: D 142 ARG cc_start: 0.9409 (mtt90) cc_final: 0.9149 (ptp-110) REVERT: E 59 GLU cc_start: 0.8910 (pm20) cc_final: 0.8691 (pm20) REVERT: E 60 LEU cc_start: 0.9326 (mt) cc_final: 0.8955 (mt) REVERT: E 85 GLN cc_start: 0.9478 (mt0) cc_final: 0.9273 (mt0) REVERT: E 105 GLU cc_start: 0.8501 (pp20) cc_final: 0.8174 (pp20) REVERT: E 106 ASP cc_start: 0.8806 (m-30) cc_final: 0.8126 (m-30) REVERT: E 133 GLU cc_start: 0.9080 (pm20) cc_final: 0.8851 (pm20) REVERT: E 134 ARG cc_start: 0.8557 (mmp-170) cc_final: 0.8260 (tpp-160) REVERT: F 22 LEU cc_start: 0.8412 (tt) cc_final: 0.8182 (tp) REVERT: F 44 LYS cc_start: 0.9261 (mtpt) cc_final: 0.8729 (mtpp) REVERT: F 79 LYS cc_start: 0.9165 (mttp) cc_final: 0.8870 (mtmm) REVERT: F 85 ASP cc_start: 0.9228 (m-30) cc_final: 0.8991 (m-30) REVERT: F 88 TYR cc_start: 0.9449 (m-10) cc_final: 0.9134 (m-80) REVERT: G 36 LYS cc_start: 0.9686 (tttt) cc_final: 0.9441 (ttmm) REVERT: G 56 GLU cc_start: 0.8884 (tt0) cc_final: 0.8528 (tt0) REVERT: G 61 GLU cc_start: 0.9191 (tp30) cc_final: 0.8939 (tp30) REVERT: G 64 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8135 (tm-30) REVERT: H 69 GLN cc_start: 0.9489 (pt0) cc_final: 0.9186 (pp30) REVERT: H 101 GLN cc_start: 0.8527 (pp30) cc_final: 0.6948 (pp30) REVERT: H 105 TYR cc_start: 0.8398 (m-10) cc_final: 0.6444 (m-10) REVERT: H 118 MET cc_start: 0.9143 (mmt) cc_final: 0.8908 (mmm) REVERT: H 138 ASN cc_start: 0.9589 (m-40) cc_final: 0.9367 (m110) REVERT: H 142 ARG cc_start: 0.9510 (ttm-80) cc_final: 0.8742 (ttm110) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1268 time to fit residues: 44.5316 Evaluate side-chains 236 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS C 94 ASN D 104 HIS D 150 GLN F 27 GLN G 84 GLN H 89 HIS H 104 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.074098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.046595 restraints weight = 47858.364| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.82 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12105 Z= 0.169 Angle : 0.643 8.337 17481 Z= 0.369 Chirality : 0.037 0.220 1995 Planarity : 0.005 0.053 1303 Dihedral : 31.535 178.603 3719 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.44 % Allowed : 18.72 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.30), residues: 737 helix: 0.64 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -2.82 (0.37), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 32 TYR 0.029 0.002 TYR B 88 PHE 0.008 0.001 PHE D 63 TRP 0.001 0.000 TRP D 149 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00368 (12105) covalent geometry : angle 0.64259 (17481) hydrogen bonds : bond 0.05135 ( 724) hydrogen bonds : angle 3.57771 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 280 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9144 (pm20) cc_final: 0.8864 (pm20) REVERT: A 73 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7673 (tt0) REVERT: A 93 GLN cc_start: 0.9060 (tp40) cc_final: 0.8815 (tp40) REVERT: A 110 CYS cc_start: 0.8492 (t) cc_final: 0.8095 (t) REVERT: B 59 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8537 (tttm) REVERT: B 63 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8652 (mt-10) REVERT: C 16 THR cc_start: 0.9534 (p) cc_final: 0.9032 (p) REVERT: C 17 ARG cc_start: 0.8912 (mtm180) cc_final: 0.8640 (mtp180) REVERT: C 20 ARG cc_start: 0.9019 (ttm170) cc_final: 0.8500 (ttm-80) REVERT: C 25 PHE cc_start: 0.8669 (m-80) cc_final: 0.8321 (m-80) REVERT: C 35 ARG cc_start: 0.9556 (ttp-110) cc_final: 0.9060 (ttm110) REVERT: C 36 LYS cc_start: 0.9321 (tmtt) cc_final: 0.8622 (tptt) REVERT: C 42 ARG cc_start: 0.8037 (ptp-170) cc_final: 0.7383 (ptm160) REVERT: C 56 GLU cc_start: 0.8864 (tt0) cc_final: 0.8470 (tt0) REVERT: C 72 ASP cc_start: 0.9268 (p0) cc_final: 0.8927 (p0) REVERT: C 73 ASN cc_start: 0.9519 (t0) cc_final: 0.9185 (t0) REVERT: C 77 ARG cc_start: 0.8720 (tpp80) cc_final: 0.8298 (mmm-85) REVERT: C 84 GLN cc_start: 0.9542 (tp40) cc_final: 0.9203 (tp40) REVERT: C 99 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8397 (mmp80) REVERT: C 104 GLN cc_start: 0.8397 (mp10) cc_final: 0.7642 (mp10) REVERT: D 117 GLN cc_start: 0.8684 (tm-30) cc_final: 0.7824 (tm-30) REVERT: D 118 MET cc_start: 0.9384 (mmt) cc_final: 0.8815 (mmm) REVERT: D 127 LYS cc_start: 0.9569 (tppt) cc_final: 0.9229 (tppt) REVERT: D 128 MET cc_start: 0.9396 (mtt) cc_final: 0.9185 (mtt) REVERT: E 73 GLU cc_start: 0.9200 (tt0) cc_final: 0.8607 (tt0) REVERT: E 79 LYS cc_start: 0.8665 (tttt) cc_final: 0.8398 (ttmt) REVERT: E 105 GLU cc_start: 0.8553 (pp20) cc_final: 0.8157 (pp20) REVERT: E 106 ASP cc_start: 0.9082 (m-30) cc_final: 0.8440 (m-30) REVERT: F 74 GLU cc_start: 0.9474 (tp30) cc_final: 0.9092 (tp30) REVERT: F 79 LYS cc_start: 0.9161 (mttp) cc_final: 0.8797 (mtmm) REVERT: F 85 ASP cc_start: 0.9305 (m-30) cc_final: 0.9034 (m-30) REVERT: F 88 TYR cc_start: 0.9367 (m-10) cc_final: 0.9066 (m-80) REVERT: G 36 LYS cc_start: 0.9710 (tttt) cc_final: 0.9400 (ttmm) REVERT: G 56 GLU cc_start: 0.8856 (tt0) cc_final: 0.8474 (tt0) REVERT: G 61 GLU cc_start: 0.9185 (tp30) cc_final: 0.8808 (tp30) REVERT: G 64 GLU cc_start: 0.8772 (tm-30) cc_final: 0.7905 (tm-30) REVERT: G 68 ASN cc_start: 0.9055 (m-40) cc_final: 0.8466 (m-40) REVERT: G 87 ILE cc_start: 0.9252 (tp) cc_final: 0.9032 (tp) REVERT: G 90 ASP cc_start: 0.8605 (t0) cc_final: 0.8215 (t0) REVERT: H 69 GLN cc_start: 0.9509 (pt0) cc_final: 0.9172 (pp30) REVERT: H 101 GLN cc_start: 0.8483 (pp30) cc_final: 0.7576 (pp30) REVERT: H 104 HIS cc_start: 0.8990 (t70) cc_final: 0.8407 (t-90) REVERT: H 105 TYR cc_start: 0.8477 (m-10) cc_final: 0.6807 (m-10) REVERT: H 118 MET cc_start: 0.9284 (mmt) cc_final: 0.8971 (mmm) REVERT: H 127 LYS cc_start: 0.9564 (mmmm) cc_final: 0.9326 (mmmm) REVERT: H 128 MET cc_start: 0.9416 (mtt) cc_final: 0.9094 (mtt) REVERT: H 142 ARG cc_start: 0.9414 (ttm-80) cc_final: 0.8630 (ttm110) outliers start: 9 outliers final: 5 residues processed: 281 average time/residue: 0.1251 time to fit residues: 46.0453 Evaluate side-chains 254 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 249 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.076029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.047222 restraints weight = 46844.208| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.77 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12105 Z= 0.160 Angle : 0.634 6.976 17481 Z= 0.365 Chirality : 0.037 0.178 1995 Planarity : 0.005 0.060 1303 Dihedral : 31.204 178.117 3719 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.64 % Allowed : 20.96 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.31), residues: 737 helix: 1.13 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -2.25 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 72 TYR 0.022 0.002 TYR F 98 PHE 0.009 0.001 PHE A 78 TRP 0.001 0.000 TRP D 149 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00349 (12105) covalent geometry : angle 0.63426 (17481) hydrogen bonds : bond 0.04754 ( 724) hydrogen bonds : angle 3.38960 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8478 (pm20) REVERT: A 73 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7549 (tt0) REVERT: A 93 GLN cc_start: 0.8837 (tp40) cc_final: 0.8401 (tp40) REVERT: A 110 CYS cc_start: 0.8543 (t) cc_final: 0.8216 (t) REVERT: B 59 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8668 (tttm) REVERT: B 63 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8766 (mt-10) REVERT: B 74 GLU cc_start: 0.9487 (tp30) cc_final: 0.9151 (mm-30) REVERT: C 17 ARG cc_start: 0.8882 (mtm180) cc_final: 0.8309 (mtp180) REVERT: C 20 ARG cc_start: 0.9048 (ttm170) cc_final: 0.8634 (ttm110) REVERT: C 25 PHE cc_start: 0.8690 (m-80) cc_final: 0.8129 (m-80) REVERT: C 36 LYS cc_start: 0.9100 (tmtt) cc_final: 0.8825 (tptp) REVERT: C 42 ARG cc_start: 0.8000 (ptp-170) cc_final: 0.7387 (mtm110) REVERT: C 56 GLU cc_start: 0.8870 (tt0) cc_final: 0.8341 (tt0) REVERT: C 57 TYR cc_start: 0.8688 (t80) cc_final: 0.8311 (t80) REVERT: C 64 GLU cc_start: 0.8883 (tp30) cc_final: 0.8570 (tp30) REVERT: C 72 ASP cc_start: 0.9274 (p0) cc_final: 0.8968 (p0) REVERT: C 73 ASN cc_start: 0.9426 (t0) cc_final: 0.9093 (t0) REVERT: C 79 ILE cc_start: 0.9074 (tp) cc_final: 0.8816 (tp) REVERT: C 84 GLN cc_start: 0.9537 (tp40) cc_final: 0.9117 (tp40) REVERT: C 88 ARG cc_start: 0.9372 (tpp-160) cc_final: 0.8955 (mmt180) REVERT: C 104 GLN cc_start: 0.8560 (mp10) cc_final: 0.7955 (mp10) REVERT: D 57 ASP cc_start: 0.7656 (t0) cc_final: 0.7175 (t0) REVERT: D 63 PHE cc_start: 0.9279 (m-80) cc_final: 0.8973 (m-80) REVERT: D 75 SER cc_start: 0.8083 (m) cc_final: 0.7577 (t) REVERT: D 78 GLN cc_start: 0.9362 (tp40) cc_final: 0.8992 (mm-40) REVERT: D 107 LYS cc_start: 0.9545 (mmmm) cc_final: 0.9304 (tppt) REVERT: D 117 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8206 (tm-30) REVERT: D 118 MET cc_start: 0.9273 (mmt) cc_final: 0.8806 (mmm) REVERT: D 127 LYS cc_start: 0.9572 (tppt) cc_final: 0.9299 (tppt) REVERT: E 73 GLU cc_start: 0.9143 (tt0) cc_final: 0.8510 (tt0) REVERT: E 79 LYS cc_start: 0.8736 (tttt) cc_final: 0.8451 (ttmt) REVERT: E 105 GLU cc_start: 0.8557 (pp20) cc_final: 0.8199 (pp20) REVERT: E 106 ASP cc_start: 0.9157 (m-30) cc_final: 0.8555 (m-30) REVERT: E 120 MET cc_start: 0.8765 (mmm) cc_final: 0.8136 (mpp) REVERT: F 74 GLU cc_start: 0.9530 (tp30) cc_final: 0.9108 (tp30) REVERT: F 79 LYS cc_start: 0.9050 (mttp) cc_final: 0.8756 (mtmm) REVERT: F 88 TYR cc_start: 0.9351 (m-10) cc_final: 0.8998 (m-80) REVERT: F 98 TYR cc_start: 0.8528 (m-80) cc_final: 0.7936 (m-80) REVERT: G 35 ARG cc_start: 0.9547 (ttp-110) cc_final: 0.9125 (ttm110) REVERT: G 36 LYS cc_start: 0.9613 (tttt) cc_final: 0.9319 (ttmm) REVERT: G 56 GLU cc_start: 0.8851 (tt0) cc_final: 0.8561 (tt0) REVERT: G 61 GLU cc_start: 0.9187 (tp30) cc_final: 0.8836 (tp30) REVERT: G 64 GLU cc_start: 0.8815 (tm-30) cc_final: 0.7975 (tm-30) REVERT: G 68 ASN cc_start: 0.9090 (m-40) cc_final: 0.8450 (m-40) REVERT: G 87 ILE cc_start: 0.9266 (tp) cc_final: 0.9032 (tp) REVERT: G 90 ASP cc_start: 0.8532 (t0) cc_final: 0.7841 (t0) REVERT: H 62 TYR cc_start: 0.9364 (m-80) cc_final: 0.8968 (m-80) REVERT: H 69 GLN cc_start: 0.9527 (pt0) cc_final: 0.9211 (pp30) REVERT: H 85 ASP cc_start: 0.9280 (t0) cc_final: 0.8895 (t0) REVERT: H 105 TYR cc_start: 0.8487 (m-10) cc_final: 0.7308 (m-10) REVERT: H 118 MET cc_start: 0.9246 (mmt) cc_final: 0.8932 (mmm) REVERT: H 142 ARG cc_start: 0.9423 (ttm-80) cc_final: 0.8615 (ttm110) outliers start: 29 outliers final: 14 residues processed: 282 average time/residue: 0.1203 time to fit residues: 44.9347 Evaluate side-chains 267 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 252 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN H 89 HIS H 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.074356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.045692 restraints weight = 46897.641| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.66 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12105 Z= 0.218 Angle : 0.654 8.602 17481 Z= 0.375 Chirality : 0.038 0.286 1995 Planarity : 0.005 0.061 1303 Dihedral : 31.238 177.724 3719 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.96 % Allowed : 21.12 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.32), residues: 737 helix: 1.40 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -2.04 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.015 0.002 TYR F 98 PHE 0.009 0.001 PHE E 104 TRP 0.001 0.000 TRP D 149 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00490 (12105) covalent geometry : angle 0.65373 (17481) hydrogen bonds : bond 0.05188 ( 724) hydrogen bonds : angle 3.48176 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8825 (pm20) cc_final: 0.8536 (pm20) REVERT: A 68 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8626 (tm130) REVERT: A 73 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7495 (tt0) REVERT: A 93 GLN cc_start: 0.9038 (tp40) cc_final: 0.8548 (tp40) REVERT: A 110 CYS cc_start: 0.8510 (t) cc_final: 0.8220 (t) REVERT: A 120 MET cc_start: 0.8532 (mmm) cc_final: 0.8311 (mmm) REVERT: B 59 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8759 (tttm) REVERT: B 63 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8803 (mt-10) REVERT: C 17 ARG cc_start: 0.8973 (mtm180) cc_final: 0.8450 (mtp180) REVERT: C 20 ARG cc_start: 0.9106 (ttm170) cc_final: 0.8661 (ttm110) REVERT: C 36 LYS cc_start: 0.9194 (tmtt) cc_final: 0.8595 (tptt) REVERT: C 39 TYR cc_start: 0.8472 (m-80) cc_final: 0.8189 (m-80) REVERT: C 42 ARG cc_start: 0.8025 (ptp-170) cc_final: 0.7299 (mtm110) REVERT: C 56 GLU cc_start: 0.8906 (tt0) cc_final: 0.8569 (tt0) REVERT: C 57 TYR cc_start: 0.8734 (t80) cc_final: 0.8313 (t80) REVERT: C 61 GLU cc_start: 0.8899 (tt0) cc_final: 0.8649 (tt0) REVERT: C 64 GLU cc_start: 0.8874 (tp30) cc_final: 0.8667 (tp30) REVERT: C 72 ASP cc_start: 0.9232 (p0) cc_final: 0.9009 (p0) REVERT: C 73 ASN cc_start: 0.9422 (t0) cc_final: 0.9082 (t0) REVERT: C 84 GLN cc_start: 0.9584 (tp40) cc_final: 0.9124 (tp40) REVERT: C 88 ARG cc_start: 0.9339 (tpp-160) cc_final: 0.8903 (mmt180) REVERT: C 99 ARG cc_start: 0.8855 (mmm160) cc_final: 0.8477 (mmp80) REVERT: D 75 SER cc_start: 0.8272 (m) cc_final: 0.7663 (p) REVERT: D 78 GLN cc_start: 0.9420 (tp40) cc_final: 0.9076 (mm-40) REVERT: D 87 MET cc_start: 0.8988 (ttp) cc_final: 0.8764 (ttp) REVERT: D 107 LYS cc_start: 0.9554 (mmmm) cc_final: 0.9239 (tppt) REVERT: D 117 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8314 (tm-30) REVERT: D 118 MET cc_start: 0.9342 (mmt) cc_final: 0.8945 (mmm) REVERT: D 127 LYS cc_start: 0.9569 (tppt) cc_final: 0.9333 (tppt) REVERT: E 73 GLU cc_start: 0.9081 (tt0) cc_final: 0.8230 (tt0) REVERT: E 79 LYS cc_start: 0.8703 (tttt) cc_final: 0.8418 (ttmt) REVERT: E 105 GLU cc_start: 0.8507 (pp20) cc_final: 0.8155 (pp20) REVERT: E 106 ASP cc_start: 0.9115 (m-30) cc_final: 0.8470 (m-30) REVERT: F 74 GLU cc_start: 0.9513 (tp30) cc_final: 0.9056 (tp30) REVERT: F 79 LYS cc_start: 0.9089 (mttp) cc_final: 0.8842 (mtmm) REVERT: F 88 TYR cc_start: 0.9423 (m-10) cc_final: 0.9113 (m-80) REVERT: F 98 TYR cc_start: 0.8530 (m-80) cc_final: 0.7982 (m-80) REVERT: G 36 LYS cc_start: 0.9629 (tttt) cc_final: 0.9334 (ttmm) REVERT: G 56 GLU cc_start: 0.8823 (tt0) cc_final: 0.8607 (tt0) REVERT: G 61 GLU cc_start: 0.9182 (tp30) cc_final: 0.8685 (tp30) REVERT: G 64 GLU cc_start: 0.8853 (tm-30) cc_final: 0.7974 (tm-30) REVERT: G 68 ASN cc_start: 0.9105 (m-40) cc_final: 0.8442 (m-40) REVERT: G 87 ILE cc_start: 0.9302 (tp) cc_final: 0.9092 (tp) REVERT: G 90 ASP cc_start: 0.8472 (t70) cc_final: 0.7889 (t0) REVERT: H 69 GLN cc_start: 0.9524 (pt0) cc_final: 0.9178 (pp30) REVERT: H 85 ASP cc_start: 0.9342 (t0) cc_final: 0.8898 (t0) REVERT: H 101 GLN cc_start: 0.9118 (tt0) cc_final: 0.8567 (tm-30) REVERT: H 104 HIS cc_start: 0.9020 (t70) cc_final: 0.8409 (t-90) REVERT: H 105 TYR cc_start: 0.8603 (m-10) cc_final: 0.7036 (m-10) REVERT: H 118 MET cc_start: 0.9234 (mmt) cc_final: 0.8904 (mmm) REVERT: H 142 ARG cc_start: 0.9485 (ttm-80) cc_final: 0.8670 (ttm110) outliers start: 31 outliers final: 21 residues processed: 270 average time/residue: 0.1218 time to fit residues: 43.8019 Evaluate side-chains 267 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN G 94 ASN H 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.074181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.045717 restraints weight = 46832.728| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.65 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12105 Z= 0.223 Angle : 0.663 8.493 17481 Z= 0.380 Chirality : 0.039 0.225 1995 Planarity : 0.004 0.061 1303 Dihedral : 31.216 177.597 3719 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.28 % Allowed : 24.16 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.32), residues: 737 helix: 1.56 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.74 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 108 TYR 0.017 0.002 TYR G 39 PHE 0.010 0.001 PHE E 104 TRP 0.001 0.000 TRP D 149 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00504 (12105) covalent geometry : angle 0.66264 (17481) hydrogen bonds : bond 0.05137 ( 724) hydrogen bonds : angle 3.46590 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8758 (pm20) cc_final: 0.8558 (pm20) REVERT: A 73 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7515 (tt0) REVERT: A 93 GLN cc_start: 0.8996 (tp40) cc_final: 0.8558 (tp40) REVERT: A 120 MET cc_start: 0.8588 (mmm) cc_final: 0.8321 (mmm) REVERT: B 59 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8689 (tttm) REVERT: B 63 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8716 (mt-10) REVERT: C 17 ARG cc_start: 0.8996 (mtm180) cc_final: 0.8459 (mtp180) REVERT: C 20 ARG cc_start: 0.9106 (ttm170) cc_final: 0.8673 (ttm110) REVERT: C 25 PHE cc_start: 0.8800 (m-80) cc_final: 0.8078 (m-80) REVERT: C 36 LYS cc_start: 0.9172 (tmtt) cc_final: 0.8857 (tptp) REVERT: C 39 TYR cc_start: 0.8595 (m-80) cc_final: 0.8330 (m-80) REVERT: C 56 GLU cc_start: 0.9007 (tt0) cc_final: 0.8508 (tt0) REVERT: C 57 TYR cc_start: 0.8617 (t80) cc_final: 0.8263 (t80) REVERT: C 72 ASP cc_start: 0.9200 (p0) cc_final: 0.8968 (p0) REVERT: C 73 ASN cc_start: 0.9381 (t0) cc_final: 0.9022 (t0) REVERT: C 84 GLN cc_start: 0.9551 (tp40) cc_final: 0.9149 (tp40) REVERT: C 92 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.9042 (pt0) REVERT: C 99 ARG cc_start: 0.8834 (mmm160) cc_final: 0.8421 (mmp80) REVERT: C 104 GLN cc_start: 0.8667 (mp10) cc_final: 0.7908 (mp10) REVERT: D 65 ARG cc_start: 0.9392 (ttm110) cc_final: 0.9130 (ttp-110) REVERT: D 75 SER cc_start: 0.8218 (m) cc_final: 0.7557 (p) REVERT: D 87 MET cc_start: 0.8989 (ttp) cc_final: 0.8731 (ttp) REVERT: D 107 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9255 (tppt) REVERT: D 117 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8216 (tm-30) REVERT: D 118 MET cc_start: 0.9316 (mmt) cc_final: 0.8911 (mmm) REVERT: D 127 LYS cc_start: 0.9560 (tppt) cc_final: 0.9342 (tppt) REVERT: D 128 MET cc_start: 0.9433 (mtp) cc_final: 0.8159 (mtp) REVERT: E 73 GLU cc_start: 0.9006 (tt0) cc_final: 0.8278 (tt0) REVERT: E 79 LYS cc_start: 0.8677 (tttt) cc_final: 0.8401 (ttmt) REVERT: E 105 GLU cc_start: 0.8569 (pp20) cc_final: 0.8219 (pp20) REVERT: E 106 ASP cc_start: 0.9053 (m-30) cc_final: 0.8429 (m-30) REVERT: F 74 GLU cc_start: 0.9528 (tp30) cc_final: 0.9166 (tp30) REVERT: F 79 LYS cc_start: 0.9119 (mttp) cc_final: 0.8876 (mtmm) REVERT: F 88 TYR cc_start: 0.9432 (m-10) cc_final: 0.9017 (m-80) REVERT: F 98 TYR cc_start: 0.8574 (m-10) cc_final: 0.7927 (m-80) REVERT: G 36 LYS cc_start: 0.9615 (tttt) cc_final: 0.9325 (ttmm) REVERT: G 56 GLU cc_start: 0.8791 (tt0) cc_final: 0.8551 (tt0) REVERT: G 61 GLU cc_start: 0.9184 (tp30) cc_final: 0.8682 (tp30) REVERT: G 64 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8010 (tm-30) REVERT: G 68 ASN cc_start: 0.9113 (m-40) cc_final: 0.8457 (m-40) REVERT: G 87 ILE cc_start: 0.9304 (tp) cc_final: 0.8989 (tp) REVERT: G 90 ASP cc_start: 0.8315 (t70) cc_final: 0.7865 (t0) REVERT: G 104 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8869 (mm-40) REVERT: H 62 TYR cc_start: 0.9490 (m-80) cc_final: 0.8904 (m-80) REVERT: H 69 GLN cc_start: 0.9546 (pt0) cc_final: 0.9203 (pp30) REVERT: H 101 GLN cc_start: 0.9179 (tt0) cc_final: 0.8527 (tm-30) REVERT: H 105 TYR cc_start: 0.8556 (m-10) cc_final: 0.6911 (m-10) REVERT: H 118 MET cc_start: 0.9217 (mmt) cc_final: 0.8877 (mmm) REVERT: H 142 ARG cc_start: 0.9483 (ttm-80) cc_final: 0.8683 (ttm110) outliers start: 33 outliers final: 21 residues processed: 269 average time/residue: 0.1292 time to fit residues: 46.1785 Evaluate side-chains 262 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 82 optimal weight: 10.0000 chunk 71 optimal weight: 40.0000 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN G 94 ASN H 89 HIS H 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.076325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047446 restraints weight = 46973.652| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.78 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12105 Z= 0.165 Angle : 0.653 9.050 17481 Z= 0.374 Chirality : 0.038 0.199 1995 Planarity : 0.004 0.062 1303 Dihedral : 31.031 177.544 3719 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.64 % Allowed : 24.96 % Favored : 70.40 % 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: 1.02 (0.32), residues: 737 helix: 1.60 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.64 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 108 TYR 0.024 0.002 TYR D 105 PHE 0.006 0.001 PHE D 63 TRP 0.001 0.000 TRP D 149 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00365 (12105) covalent geometry : angle 0.65348 (17481) hydrogen bonds : bond 0.04618 ( 724) hydrogen bonds : angle 3.27321 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 270 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7458 (tt0) REVERT: A 93 GLN cc_start: 0.8966 (tp40) cc_final: 0.8402 (tp40) REVERT: A 94 GLU cc_start: 0.9436 (OUTLIER) cc_final: 0.9057 (tp30) REVERT: A 120 MET cc_start: 0.8541 (mmm) cc_final: 0.8296 (mmm) REVERT: B 59 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8563 (tptp) REVERT: B 63 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8685 (mt-10) REVERT: B 74 GLU cc_start: 0.9507 (mm-30) cc_final: 0.9250 (mm-30) REVERT: B 84 MET cc_start: 0.8450 (tpp) cc_final: 0.8047 (tpp) REVERT: C 17 ARG cc_start: 0.8981 (mtm180) cc_final: 0.8389 (mtp180) REVERT: C 20 ARG cc_start: 0.9124 (ttm170) cc_final: 0.8718 (ttm110) REVERT: C 25 PHE cc_start: 0.8796 (m-80) cc_final: 0.8016 (m-80) REVERT: C 36 LYS cc_start: 0.9146 (tmtt) cc_final: 0.8825 (tptp) REVERT: C 41 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7303 (tm-30) REVERT: C 42 ARG cc_start: 0.7469 (ptp-110) cc_final: 0.6982 (mtp-110) REVERT: C 56 GLU cc_start: 0.8983 (tt0) cc_final: 0.8454 (tt0) REVERT: C 57 TYR cc_start: 0.8638 (t80) cc_final: 0.8406 (t80) REVERT: C 64 GLU cc_start: 0.8820 (tp30) cc_final: 0.8508 (tp30) REVERT: C 71 ARG cc_start: 0.9515 (ttm-80) cc_final: 0.8945 (mmt90) REVERT: C 73 ASN cc_start: 0.9346 (t0) cc_final: 0.8839 (t0) REVERT: C 75 LYS cc_start: 0.8674 (mttm) cc_final: 0.8415 (mmtm) REVERT: C 77 ARG cc_start: 0.8925 (tpp80) cc_final: 0.8313 (mmm-85) REVERT: C 84 GLN cc_start: 0.9531 (tp40) cc_final: 0.9116 (tp40) REVERT: C 92 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.8994 (pt0) REVERT: C 104 GLN cc_start: 0.8725 (mp10) cc_final: 0.7940 (mp10) REVERT: D 75 SER cc_start: 0.8108 (m) cc_final: 0.7613 (p) REVERT: D 78 GLN cc_start: 0.9440 (tp40) cc_final: 0.9228 (mm-40) REVERT: D 87 MET cc_start: 0.9042 (ttp) cc_final: 0.8828 (ttp) REVERT: D 107 LYS cc_start: 0.9576 (mmmm) cc_final: 0.9213 (tppt) REVERT: D 117 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8252 (tm-30) REVERT: D 118 MET cc_start: 0.9312 (mmt) cc_final: 0.8907 (mmm) REVERT: D 127 LYS cc_start: 0.9547 (tppt) cc_final: 0.9299 (tppt) REVERT: D 128 MET cc_start: 0.9377 (mtp) cc_final: 0.8047 (mtp) REVERT: E 73 GLU cc_start: 0.8936 (tt0) cc_final: 0.8193 (tt0) REVERT: E 79 LYS cc_start: 0.8586 (tttt) cc_final: 0.8222 (ttmt) REVERT: E 85 GLN cc_start: 0.9170 (mt0) cc_final: 0.8890 (mt0) REVERT: E 105 GLU cc_start: 0.8554 (pp20) cc_final: 0.8269 (pp20) REVERT: E 106 ASP cc_start: 0.9073 (m-30) cc_final: 0.8452 (m-30) REVERT: E 120 MET cc_start: 0.8775 (mmm) cc_final: 0.8152 (mpp) REVERT: F 74 GLU cc_start: 0.9531 (tp30) cc_final: 0.9053 (tp30) REVERT: F 79 LYS cc_start: 0.9100 (mttp) cc_final: 0.8846 (mtmm) REVERT: F 88 TYR cc_start: 0.9391 (m-10) cc_final: 0.9118 (m-80) REVERT: F 98 TYR cc_start: 0.8652 (m-10) cc_final: 0.8100 (m-80) REVERT: G 20 ARG cc_start: 0.9036 (mtm-85) cc_final: 0.8546 (ttm-80) REVERT: G 36 LYS cc_start: 0.9591 (tttt) cc_final: 0.9346 (ttmm) REVERT: G 56 GLU cc_start: 0.8737 (tt0) cc_final: 0.8492 (tt0) REVERT: G 61 GLU cc_start: 0.9110 (tp30) cc_final: 0.8600 (tp30) REVERT: G 64 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8029 (tm-30) REVERT: G 68 ASN cc_start: 0.9095 (m-40) cc_final: 0.8368 (m-40) REVERT: G 87 ILE cc_start: 0.9353 (tp) cc_final: 0.9082 (tp) REVERT: G 88 ARG cc_start: 0.9419 (mmt-90) cc_final: 0.9127 (tpp80) REVERT: G 90 ASP cc_start: 0.8290 (t70) cc_final: 0.7802 (t0) REVERT: H 62 TYR cc_start: 0.9432 (m-80) cc_final: 0.8906 (m-80) REVERT: H 69 GLN cc_start: 0.9526 (pt0) cc_final: 0.9131 (pp30) REVERT: H 85 ASP cc_start: 0.9306 (t0) cc_final: 0.8924 (t0) REVERT: H 105 TYR cc_start: 0.8512 (m-10) cc_final: 0.7246 (m-10) REVERT: H 118 MET cc_start: 0.9224 (mmt) cc_final: 0.8897 (mmm) REVERT: H 142 ARG cc_start: 0.9450 (ttm-80) cc_final: 0.8657 (ttm110) outliers start: 29 outliers final: 20 residues processed: 284 average time/residue: 0.1289 time to fit residues: 48.4549 Evaluate side-chains 277 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 104 HIS H 89 HIS H 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.076036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.047072 restraints weight = 46984.388| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.73 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12105 Z= 0.190 Angle : 0.683 7.864 17481 Z= 0.388 Chirality : 0.038 0.221 1995 Planarity : 0.005 0.064 1303 Dihedral : 31.024 177.503 3719 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.32 % Allowed : 28.80 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.31), residues: 737 helix: 1.52 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.65 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 108 TYR 0.027 0.002 TYR C 39 PHE 0.007 0.001 PHE E 104 TRP 0.000 0.000 TRP D 149 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00429 (12105) covalent geometry : angle 0.68251 (17481) hydrogen bonds : bond 0.04826 ( 724) hydrogen bonds : angle 3.38425 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7393 (tt0) REVERT: A 93 GLN cc_start: 0.8897 (tp40) cc_final: 0.8426 (tp40) REVERT: A 94 GLU cc_start: 0.9458 (OUTLIER) cc_final: 0.9093 (tp30) REVERT: A 120 MET cc_start: 0.8595 (mmm) cc_final: 0.8309 (mmm) REVERT: B 59 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8569 (tptp) REVERT: B 63 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8672 (mt-10) REVERT: C 17 ARG cc_start: 0.8989 (mtm180) cc_final: 0.8400 (mtp180) REVERT: C 20 ARG cc_start: 0.9107 (ttm170) cc_final: 0.8713 (ttm110) REVERT: C 25 PHE cc_start: 0.8880 (m-80) cc_final: 0.8528 (m-80) REVERT: C 36 LYS cc_start: 0.9107 (tmtt) cc_final: 0.8802 (tptp) REVERT: C 56 GLU cc_start: 0.8992 (tt0) cc_final: 0.8660 (tt0) REVERT: C 71 ARG cc_start: 0.9497 (ttm-80) cc_final: 0.8944 (mmt90) REVERT: C 73 ASN cc_start: 0.9301 (t0) cc_final: 0.8721 (t0) REVERT: C 75 LYS cc_start: 0.8645 (mttm) cc_final: 0.8390 (mmtm) REVERT: C 77 ARG cc_start: 0.8910 (tpp80) cc_final: 0.8277 (mmm-85) REVERT: C 84 GLN cc_start: 0.9538 (tp40) cc_final: 0.9076 (tp40) REVERT: C 92 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8947 (pt0) REVERT: C 99 ARG cc_start: 0.8841 (mmm160) cc_final: 0.8405 (mmp80) REVERT: C 104 GLN cc_start: 0.8764 (mp10) cc_final: 0.7938 (mp10) REVERT: D 65 ARG cc_start: 0.9351 (ttm110) cc_final: 0.9091 (ttm110) REVERT: D 75 SER cc_start: 0.8029 (m) cc_final: 0.7530 (p) REVERT: D 78 GLN cc_start: 0.9438 (tp40) cc_final: 0.9218 (mm-40) REVERT: D 87 MET cc_start: 0.9047 (ttp) cc_final: 0.8794 (ttp) REVERT: D 107 LYS cc_start: 0.9547 (mmmm) cc_final: 0.9218 (tppt) REVERT: D 117 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8255 (tm-30) REVERT: D 118 MET cc_start: 0.9355 (mmt) cc_final: 0.8899 (mmm) REVERT: D 127 LYS cc_start: 0.9547 (tppt) cc_final: 0.9320 (tppt) REVERT: D 128 MET cc_start: 0.9355 (mtp) cc_final: 0.7890 (mtp) REVERT: E 73 GLU cc_start: 0.8950 (tt0) cc_final: 0.8177 (tt0) REVERT: E 79 LYS cc_start: 0.8503 (tttt) cc_final: 0.8223 (ttmt) REVERT: E 105 GLU cc_start: 0.8575 (pp20) cc_final: 0.8236 (pp20) REVERT: E 106 ASP cc_start: 0.9082 (m-30) cc_final: 0.8448 (m-30) REVERT: E 120 MET cc_start: 0.8777 (mmm) cc_final: 0.8117 (mpp) REVERT: F 74 GLU cc_start: 0.9535 (tp30) cc_final: 0.9159 (tp30) REVERT: F 79 LYS cc_start: 0.9099 (mttp) cc_final: 0.8831 (mtmm) REVERT: F 88 TYR cc_start: 0.9348 (m-10) cc_final: 0.9086 (m-80) REVERT: F 98 TYR cc_start: 0.8646 (m-10) cc_final: 0.8018 (m-80) REVERT: G 20 ARG cc_start: 0.9092 (mtm-85) cc_final: 0.8581 (ttm-80) REVERT: G 36 LYS cc_start: 0.9610 (tttt) cc_final: 0.9281 (ttmm) REVERT: G 56 GLU cc_start: 0.8747 (tt0) cc_final: 0.8467 (tt0) REVERT: G 61 GLU cc_start: 0.9163 (tp30) cc_final: 0.8665 (tp30) REVERT: G 64 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8018 (tm-30) REVERT: G 68 ASN cc_start: 0.9053 (m-40) cc_final: 0.8392 (m-40) REVERT: G 87 ILE cc_start: 0.9335 (tp) cc_final: 0.8978 (tp) REVERT: G 88 ARG cc_start: 0.9441 (mmt-90) cc_final: 0.9009 (tpp80) REVERT: G 90 ASP cc_start: 0.8217 (t70) cc_final: 0.7904 (t0) REVERT: H 62 TYR cc_start: 0.9476 (m-80) cc_final: 0.8898 (m-80) REVERT: H 69 GLN cc_start: 0.9512 (pt0) cc_final: 0.9136 (pp30) REVERT: H 85 ASP cc_start: 0.9282 (t0) cc_final: 0.8922 (t0) REVERT: H 101 GLN cc_start: 0.9152 (tt0) cc_final: 0.8402 (tm-30) REVERT: H 105 TYR cc_start: 0.8622 (m-10) cc_final: 0.7093 (m-10) REVERT: H 118 MET cc_start: 0.9204 (mmt) cc_final: 0.8869 (mmm) REVERT: H 142 ARG cc_start: 0.9448 (ttm-80) cc_final: 0.8641 (ttm110) outliers start: 27 outliers final: 19 residues processed: 270 average time/residue: 0.1333 time to fit residues: 47.6348 Evaluate side-chains 272 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 HIS H 104 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.076472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.047362 restraints weight = 46645.386| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.83 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12105 Z= 0.180 Angle : 0.689 9.859 17481 Z= 0.390 Chirality : 0.038 0.214 1995 Planarity : 0.005 0.064 1303 Dihedral : 30.959 177.323 3719 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.16 % Allowed : 30.56 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.31), residues: 737 helix: 1.41 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.59 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 108 TYR 0.025 0.002 TYR C 39 PHE 0.006 0.001 PHE E 104 TRP 0.000 0.000 TRP D 149 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00405 (12105) covalent geometry : angle 0.68862 (17481) hydrogen bonds : bond 0.04674 ( 724) hydrogen bonds : angle 3.39469 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9126 (pt0) cc_final: 0.8587 (pp20) REVERT: A 73 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7396 (tt0) REVERT: A 93 GLN cc_start: 0.8877 (tp40) cc_final: 0.8374 (tp40) REVERT: A 94 GLU cc_start: 0.9450 (OUTLIER) cc_final: 0.9075 (tp30) REVERT: A 120 MET cc_start: 0.8605 (mmm) cc_final: 0.8317 (mmm) REVERT: B 59 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8624 (tptp) REVERT: B 63 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8643 (mt-10) REVERT: C 17 ARG cc_start: 0.8982 (mtm180) cc_final: 0.8442 (mtp180) REVERT: C 20 ARG cc_start: 0.9128 (ttm170) cc_final: 0.8774 (ttm110) REVERT: C 25 PHE cc_start: 0.8888 (m-80) cc_final: 0.8525 (m-80) REVERT: C 36 LYS cc_start: 0.9087 (tmtt) cc_final: 0.8865 (tptp) REVERT: C 41 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7378 (tm-30) REVERT: C 42 ARG cc_start: 0.7729 (ptp-170) cc_final: 0.6937 (mtm110) REVERT: C 56 GLU cc_start: 0.8979 (tt0) cc_final: 0.8638 (tt0) REVERT: C 64 GLU cc_start: 0.8931 (tp30) cc_final: 0.8642 (tp30) REVERT: C 71 ARG cc_start: 0.9476 (ttm-80) cc_final: 0.9008 (mmt90) REVERT: C 73 ASN cc_start: 0.9324 (t0) cc_final: 0.8534 (t0) REVERT: C 75 LYS cc_start: 0.8667 (mttm) cc_final: 0.8318 (mmtp) REVERT: C 77 ARG cc_start: 0.8970 (tpp80) cc_final: 0.8327 (mmm-85) REVERT: C 84 GLN cc_start: 0.9565 (tp40) cc_final: 0.8831 (tp40) REVERT: C 88 ARG cc_start: 0.9359 (tpp-160) cc_final: 0.8952 (mmt180) REVERT: C 92 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8927 (pt0) REVERT: C 99 ARG cc_start: 0.8798 (mmm160) cc_final: 0.8416 (mmp80) REVERT: C 102 ILE cc_start: 0.9102 (mp) cc_final: 0.8831 (mp) REVERT: C 104 GLN cc_start: 0.8793 (mp10) cc_final: 0.7950 (mp10) REVERT: D 65 ARG cc_start: 0.9332 (ttm110) cc_final: 0.9089 (ttm110) REVERT: D 75 SER cc_start: 0.7995 (m) cc_final: 0.7451 (p) REVERT: D 78 GLN cc_start: 0.9441 (tp40) cc_final: 0.9225 (mm-40) REVERT: D 85 ASP cc_start: 0.8814 (t0) cc_final: 0.8207 (t0) REVERT: D 87 MET cc_start: 0.9046 (ttp) cc_final: 0.8780 (ttp) REVERT: D 89 HIS cc_start: 0.9077 (m-70) cc_final: 0.8540 (m-70) REVERT: D 107 LYS cc_start: 0.9548 (mmmm) cc_final: 0.9279 (tppt) REVERT: D 117 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8153 (tm-30) REVERT: D 118 MET cc_start: 0.9353 (mmt) cc_final: 0.8897 (mmm) REVERT: D 127 LYS cc_start: 0.9557 (tppt) cc_final: 0.9308 (tppt) REVERT: D 128 MET cc_start: 0.9390 (mtp) cc_final: 0.8442 (mtp) REVERT: D 142 ARG cc_start: 0.9548 (mtt90) cc_final: 0.9232 (mtt-85) REVERT: E 73 GLU cc_start: 0.8925 (tt0) cc_final: 0.8175 (tt0) REVERT: E 79 LYS cc_start: 0.8347 (tttt) cc_final: 0.8000 (ttmt) REVERT: E 105 GLU cc_start: 0.8585 (pp20) cc_final: 0.8276 (pp20) REVERT: E 106 ASP cc_start: 0.9105 (m-30) cc_final: 0.8510 (m-30) REVERT: F 74 GLU cc_start: 0.9529 (tp30) cc_final: 0.9144 (tp30) REVERT: F 79 LYS cc_start: 0.9110 (mttp) cc_final: 0.8843 (mtmm) REVERT: F 88 TYR cc_start: 0.9397 (m-10) cc_final: 0.9019 (m-80) REVERT: F 98 TYR cc_start: 0.8702 (m-10) cc_final: 0.8032 (m-80) REVERT: G 56 GLU cc_start: 0.8736 (tt0) cc_final: 0.8436 (tt0) REVERT: G 61 GLU cc_start: 0.9134 (tp30) cc_final: 0.8625 (tp30) REVERT: G 64 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8015 (tm-30) REVERT: G 68 ASN cc_start: 0.9066 (m-40) cc_final: 0.8400 (m-40) REVERT: G 87 ILE cc_start: 0.9340 (tp) cc_final: 0.9113 (tp) REVERT: G 88 ARG cc_start: 0.9421 (mmt-90) cc_final: 0.9096 (tpp80) REVERT: G 90 ASP cc_start: 0.8227 (t70) cc_final: 0.7926 (t0) REVERT: H 62 TYR cc_start: 0.9463 (m-80) cc_final: 0.8916 (m-80) REVERT: H 69 GLN cc_start: 0.9510 (pt0) cc_final: 0.9138 (pp30) REVERT: H 85 ASP cc_start: 0.9267 (t0) cc_final: 0.8901 (t0) REVERT: H 101 GLN cc_start: 0.9078 (tt0) cc_final: 0.8300 (tm-30) REVERT: H 105 TYR cc_start: 0.8653 (m-10) cc_final: 0.7056 (m-10) REVERT: H 118 MET cc_start: 0.9226 (mmt) cc_final: 0.8879 (mmm) REVERT: H 142 ARG cc_start: 0.9442 (ttm-80) cc_final: 0.8635 (ttm110) outliers start: 26 outliers final: 21 residues processed: 273 average time/residue: 0.1333 time to fit residues: 47.9724 Evaluate side-chains 276 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 0.1980 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 94 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 110 ASN D 104 HIS H 89 HIS H 104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.077226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048168 restraints weight = 45678.222| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.76 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12105 Z= 0.177 Angle : 0.684 8.356 17481 Z= 0.389 Chirality : 0.038 0.230 1995 Planarity : 0.005 0.080 1303 Dihedral : 30.886 177.245 3719 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.84 % Allowed : 31.84 % Favored : 64.32 % 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: 0.88 (0.31), residues: 737 helix: 1.40 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.46 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 108 TYR 0.024 0.002 TYR G 39 PHE 0.005 0.001 PHE E 104 TRP 0.000 0.000 TRP D 149 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00397 (12105) covalent geometry : angle 0.68421 (17481) hydrogen bonds : bond 0.04657 ( 724) hydrogen bonds : angle 3.37176 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9132 (pt0) cc_final: 0.8585 (pp20) REVERT: A 73 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7404 (tt0) REVERT: A 93 GLN cc_start: 0.8816 (tp40) cc_final: 0.8441 (tp40) REVERT: A 94 GLU cc_start: 0.9429 (OUTLIER) cc_final: 0.9042 (tp30) REVERT: A 120 MET cc_start: 0.8611 (mmm) cc_final: 0.8322 (mmm) REVERT: B 59 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8558 (tptp) REVERT: B 63 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8640 (mt-10) REVERT: C 17 ARG cc_start: 0.9027 (mtm180) cc_final: 0.8421 (mtp180) REVERT: C 20 ARG cc_start: 0.9189 (ttm170) cc_final: 0.8815 (ttm110) REVERT: C 25 PHE cc_start: 0.8901 (m-80) cc_final: 0.8530 (m-80) REVERT: C 36 LYS cc_start: 0.9173 (tmtt) cc_final: 0.8900 (tptp) REVERT: C 42 ARG cc_start: 0.7794 (ptp-170) cc_final: 0.6991 (mtm110) REVERT: C 56 GLU cc_start: 0.8973 (tt0) cc_final: 0.8624 (tt0) REVERT: C 64 GLU cc_start: 0.8966 (tp30) cc_final: 0.8650 (tp30) REVERT: C 71 ARG cc_start: 0.9479 (ttm-80) cc_final: 0.9013 (mmt90) REVERT: C 73 ASN cc_start: 0.9306 (t0) cc_final: 0.8441 (t0) REVERT: C 75 LYS cc_start: 0.8678 (mttm) cc_final: 0.8349 (mmtp) REVERT: C 77 ARG cc_start: 0.8936 (tpp80) cc_final: 0.8522 (mmm-85) REVERT: C 84 GLN cc_start: 0.9554 (tp40) cc_final: 0.8764 (tp40) REVERT: C 88 ARG cc_start: 0.9291 (tpp-160) cc_final: 0.8909 (mmt180) REVERT: C 92 GLU cc_start: 0.9337 (OUTLIER) cc_final: 0.8972 (pt0) REVERT: C 99 ARG cc_start: 0.8778 (mmm160) cc_final: 0.8415 (mmp80) REVERT: C 102 ILE cc_start: 0.9074 (mp) cc_final: 0.8805 (mp) REVERT: C 104 GLN cc_start: 0.8809 (mp10) cc_final: 0.8001 (mp10) REVERT: D 65 ARG cc_start: 0.9333 (ttm110) cc_final: 0.9084 (ttm110) REVERT: D 78 GLN cc_start: 0.9459 (tp40) cc_final: 0.9184 (mm-40) REVERT: D 85 ASP cc_start: 0.8836 (t0) cc_final: 0.8218 (t0) REVERT: D 87 MET cc_start: 0.9070 (ttp) cc_final: 0.8807 (ttp) REVERT: D 89 HIS cc_start: 0.9089 (m-70) cc_final: 0.8534 (m-70) REVERT: D 107 LYS cc_start: 0.9577 (mmmm) cc_final: 0.9301 (tppt) REVERT: D 117 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8141 (tm-30) REVERT: D 118 MET cc_start: 0.9362 (mmt) cc_final: 0.8942 (mmm) REVERT: D 127 LYS cc_start: 0.9554 (tppt) cc_final: 0.9328 (tppt) REVERT: D 128 MET cc_start: 0.9310 (mtp) cc_final: 0.8432 (mtp) REVERT: E 73 GLU cc_start: 0.8911 (tt0) cc_final: 0.8146 (tt0) REVERT: E 79 LYS cc_start: 0.8285 (tttt) cc_final: 0.7955 (ttmt) REVERT: E 105 GLU cc_start: 0.8545 (pp20) cc_final: 0.8227 (pp20) REVERT: E 106 ASP cc_start: 0.9104 (m-30) cc_final: 0.8514 (m-30) REVERT: F 74 GLU cc_start: 0.9529 (tp30) cc_final: 0.9139 (tp30) REVERT: F 79 LYS cc_start: 0.9115 (mttp) cc_final: 0.8854 (mtmm) REVERT: F 88 TYR cc_start: 0.9397 (m-10) cc_final: 0.9064 (m-80) REVERT: F 98 TYR cc_start: 0.8684 (m-10) cc_final: 0.7998 (m-80) REVERT: G 56 GLU cc_start: 0.8727 (tt0) cc_final: 0.8451 (tt0) REVERT: G 61 GLU cc_start: 0.9137 (tp30) cc_final: 0.8630 (tp30) REVERT: G 64 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8057 (tm-30) REVERT: G 68 ASN cc_start: 0.9067 (m-40) cc_final: 0.8408 (m-40) REVERT: G 87 ILE cc_start: 0.9309 (tp) cc_final: 0.9065 (tp) REVERT: G 88 ARG cc_start: 0.9406 (mmt-90) cc_final: 0.9066 (tpp80) REVERT: G 90 ASP cc_start: 0.8237 (t70) cc_final: 0.8000 (t0) REVERT: H 62 TYR cc_start: 0.9477 (m-80) cc_final: 0.8917 (m-80) REVERT: H 69 GLN cc_start: 0.9508 (pt0) cc_final: 0.9126 (pp30) REVERT: H 85 ASP cc_start: 0.9240 (t0) cc_final: 0.8895 (t0) REVERT: H 101 GLN cc_start: 0.9046 (tt0) cc_final: 0.8281 (tm-30) REVERT: H 105 TYR cc_start: 0.8648 (m-10) cc_final: 0.7014 (m-10) REVERT: H 118 MET cc_start: 0.9228 (mmt) cc_final: 0.8882 (mmm) REVERT: H 142 ARG cc_start: 0.9454 (ttm-80) cc_final: 0.8643 (ttm110) outliers start: 24 outliers final: 17 residues processed: 270 average time/residue: 0.1306 time to fit residues: 46.8195 Evaluate side-chains 273 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 254 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 71 optimal weight: 40.0000 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN H 89 HIS H 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.076902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047977 restraints weight = 46647.561| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.75 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12105 Z= 0.190 Angle : 0.708 8.847 17481 Z= 0.401 Chirality : 0.038 0.235 1995 Planarity : 0.005 0.065 1303 Dihedral : 30.884 177.149 3719 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.52 % Allowed : 33.28 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.31), residues: 737 helix: 1.34 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.33 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 108 TYR 0.041 0.002 TYR D 105 PHE 0.007 0.001 PHE A 78 TRP 0.000 0.000 TRP D 149 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00430 (12105) covalent geometry : angle 0.70767 (17481) hydrogen bonds : bond 0.04778 ( 724) hydrogen bonds : angle 3.44622 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 257 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9141 (pt0) cc_final: 0.8580 (pp20) REVERT: A 93 GLN cc_start: 0.8703 (tp40) cc_final: 0.8404 (tp40) REVERT: A 94 GLU cc_start: 0.9429 (OUTLIER) cc_final: 0.9044 (tp30) REVERT: A 120 MET cc_start: 0.8603 (mmm) cc_final: 0.8304 (mmm) REVERT: B 59 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8575 (tptp) REVERT: B 63 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8641 (mt-10) REVERT: C 17 ARG cc_start: 0.9034 (mtm180) cc_final: 0.8633 (mtp180) REVERT: C 20 ARG cc_start: 0.9198 (ttm170) cc_final: 0.8742 (ttm110) REVERT: C 25 PHE cc_start: 0.8898 (m-80) cc_final: 0.8529 (m-80) REVERT: C 36 LYS cc_start: 0.9215 (tmtt) cc_final: 0.8919 (tptp) REVERT: C 42 ARG cc_start: 0.7796 (ptp-170) cc_final: 0.6885 (mtm110) REVERT: C 56 GLU cc_start: 0.8976 (tt0) cc_final: 0.8622 (tt0) REVERT: C 64 GLU cc_start: 0.8956 (tp30) cc_final: 0.8652 (tp30) REVERT: C 71 ARG cc_start: 0.9437 (ttm-80) cc_final: 0.9046 (mmt90) REVERT: C 73 ASN cc_start: 0.9341 (t0) cc_final: 0.8560 (t0) REVERT: C 75 LYS cc_start: 0.8698 (mttm) cc_final: 0.8337 (mmtp) REVERT: C 77 ARG cc_start: 0.8949 (tpp80) cc_final: 0.8488 (mmm-85) REVERT: C 84 GLN cc_start: 0.9552 (tp40) cc_final: 0.8773 (tp40) REVERT: C 88 ARG cc_start: 0.9289 (tpp-160) cc_final: 0.8908 (mmt180) REVERT: C 92 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8980 (pt0) REVERT: C 99 ARG cc_start: 0.8785 (mmm160) cc_final: 0.8415 (mmp80) REVERT: C 102 ILE cc_start: 0.9058 (mp) cc_final: 0.8796 (mp) REVERT: C 104 GLN cc_start: 0.8810 (mp10) cc_final: 0.8024 (mp10) REVERT: D 65 ARG cc_start: 0.9315 (ttm110) cc_final: 0.9043 (ttm110) REVERT: D 78 GLN cc_start: 0.9476 (tp40) cc_final: 0.9190 (mm-40) REVERT: D 85 ASP cc_start: 0.8838 (t0) cc_final: 0.8221 (t0) REVERT: D 89 HIS cc_start: 0.9071 (m-70) cc_final: 0.8519 (m-70) REVERT: D 107 LYS cc_start: 0.9554 (mmmm) cc_final: 0.9221 (tppt) REVERT: D 117 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8199 (tm-30) REVERT: D 118 MET cc_start: 0.9405 (mmt) cc_final: 0.8973 (mmm) REVERT: D 127 LYS cc_start: 0.9560 (tppt) cc_final: 0.9338 (tppt) REVERT: D 128 MET cc_start: 0.9333 (mtp) cc_final: 0.8629 (mtp) REVERT: D 142 ARG cc_start: 0.9558 (mtt90) cc_final: 0.9221 (mtt-85) REVERT: E 73 GLU cc_start: 0.8925 (tt0) cc_final: 0.8196 (tt0) REVERT: E 79 LYS cc_start: 0.8292 (tttt) cc_final: 0.7973 (ttmt) REVERT: E 105 GLU cc_start: 0.8544 (pp20) cc_final: 0.8227 (pp20) REVERT: E 106 ASP cc_start: 0.9100 (m-30) cc_final: 0.8490 (m-30) REVERT: F 74 GLU cc_start: 0.9539 (tp30) cc_final: 0.9137 (tp30) REVERT: F 79 LYS cc_start: 0.9147 (mttp) cc_final: 0.8888 (mtmm) REVERT: F 88 TYR cc_start: 0.9408 (m-10) cc_final: 0.9048 (m-80) REVERT: F 98 TYR cc_start: 0.8630 (m-10) cc_final: 0.8070 (m-80) REVERT: G 56 GLU cc_start: 0.8719 (tt0) cc_final: 0.8474 (tt0) REVERT: G 61 GLU cc_start: 0.9174 (tp30) cc_final: 0.8671 (tp30) REVERT: G 64 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8253 (tm-30) REVERT: G 87 ILE cc_start: 0.9342 (tp) cc_final: 0.9122 (tp) REVERT: G 90 ASP cc_start: 0.8280 (t70) cc_final: 0.7827 (t0) REVERT: H 62 TYR cc_start: 0.9482 (m-80) cc_final: 0.8936 (m-80) REVERT: H 69 GLN cc_start: 0.9508 (pt0) cc_final: 0.9142 (pp30) REVERT: H 85 ASP cc_start: 0.9243 (t0) cc_final: 0.8897 (t0) REVERT: H 101 GLN cc_start: 0.9033 (tt0) cc_final: 0.8285 (tm-30) REVERT: H 104 HIS cc_start: 0.9098 (t70) cc_final: 0.8898 (t-90) REVERT: H 105 TYR cc_start: 0.8633 (m-10) cc_final: 0.7074 (m-10) REVERT: H 118 MET cc_start: 0.9224 (mmt) cc_final: 0.8880 (mmm) REVERT: H 142 ARG cc_start: 0.9447 (ttm-80) cc_final: 0.8639 (ttm110) outliers start: 22 outliers final: 17 residues processed: 267 average time/residue: 0.1261 time to fit residues: 44.8499 Evaluate side-chains 269 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 250 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 25 optimal weight: 30.0000 chunk 89 optimal weight: 8.9990 chunk 71 optimal weight: 40.0000 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN D 104 HIS ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.077558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.048783 restraints weight = 46317.454| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.76 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12105 Z= 0.174 Angle : 0.706 8.613 17481 Z= 0.399 Chirality : 0.039 0.238 1995 Planarity : 0.005 0.065 1303 Dihedral : 30.838 177.209 3719 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.36 % Allowed : 33.12 % Favored : 63.52 % 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: 0.79 (0.31), residues: 737 helix: 1.29 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.39 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 108 TYR 0.047 0.003 TYR D 105 PHE 0.005 0.001 PHE D 63 TRP 0.001 0.000 TRP D 149 HIS 0.012 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00391 (12105) covalent geometry : angle 0.70607 (17481) hydrogen bonds : bond 0.04652 ( 724) hydrogen bonds : angle 3.41825 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2275.81 seconds wall clock time: 39 minutes 48.34 seconds (2388.34 seconds total)