Starting phenix.real_space_refine on Thu Sep 18 08:22:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg2_43198/09_2025/8vg2_43198.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg2_43198/09_2025/8vg2_43198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vg2_43198/09_2025/8vg2_43198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg2_43198/09_2025/8vg2_43198.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vg2_43198/09_2025/8vg2_43198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg2_43198/09_2025/8vg2_43198.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 392 5.49 5 S 21 5.16 5 C 8651 2.51 5 N 2930 2.21 5 O 3695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15689 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 936 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "H" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3998 Classifications: {'DNA': 196} Link IDs: {'rna3p': 195} Chain: "J" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 4038 Classifications: {'DNA': 196} Link IDs: {'rna3p': 195} Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 4.04, per 1000 atoms: 0.26 Number of scatterers: 15689 At special positions: 0 Unit cell: (86.592, 121.44, 195.36, 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 21 16.00 P 392 15.00 O 3695 8.00 N 2930 7.00 C 8651 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: 1.30 Conformation dependent library (CDL) restraints added in 486.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 68.0% alpha, 3.7% beta 187 base pairs and 339 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.957A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.564A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.632A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.522A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.408A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 125 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.895A 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 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.682A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 125 Processing helix chain 'O' and resid 174 through 186 removed outlier: 3.825A pdb=" N ALA O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.801A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 Processing helix chain 'O' and resid 248 through 251 Processing helix chain 'U' and resid 38 through 51 removed outlier: 3.606A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 69 Processing helix chain 'U' and resid 71 through 74 Processing helix chain 'U' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.012A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.578A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.259A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.838A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.940A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'O' and resid 228 through 231 removed outlier: 3.538A pdb=" N TYR O 243 " --> pdb=" O VAL O 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 56 through 57 486 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 471 hydrogen bonds 942 hydrogen bond angles 0 basepair planarities 187 basepair parallelities 339 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3115 1.33 - 1.45: 5281 1.45 - 1.57: 7566 1.57 - 1.69: 782 1.69 - 1.81: 35 Bond restraints: 16779 Sorted by residual: bond pdb=" N LYS H 28 " pdb=" CA LYS H 28 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 bond pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N LYS A 36 " pdb=" CA LYS A 36 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N LYS G 9 " pdb=" CA LYS G 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LYS D 30 " pdb=" CA LYS D 30 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 16774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 22684 1.16 - 2.31: 1300 2.31 - 3.47: 303 3.47 - 4.63: 29 4.63 - 5.78: 9 Bond angle restraints: 24325 Sorted by residual: angle pdb=" CA TRP O 214 " pdb=" CB TRP O 214 " pdb=" CG TRP O 214 " ideal model delta sigma weight residual 113.60 119.13 -5.53 1.90e+00 2.77e-01 8.48e+00 angle pdb=" C2' DT I 88 " pdb=" C1' DT I 88 " pdb=" N1 DT I 88 " ideal model delta sigma weight residual 113.50 117.71 -4.21 1.50e+00 4.44e-01 7.88e+00 angle pdb=" C2' DT J 131 " pdb=" C1' DT J 131 " pdb=" N1 DT J 131 " ideal model delta sigma weight residual 113.50 117.59 -4.09 1.50e+00 4.44e-01 7.42e+00 angle pdb=" C2' DC I 151 " pdb=" C1' DC I 151 " pdb=" N1 DC I 151 " ideal model delta sigma weight residual 113.50 117.30 -3.80 1.50e+00 4.44e-01 6.42e+00 angle pdb=" C2' DC J 50 " pdb=" C1' DC J 50 " pdb=" N1 DC J 50 " ideal model delta sigma weight residual 113.50 117.09 -3.59 1.50e+00 4.44e-01 5.74e+00 ... (remaining 24320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 6209 17.10 - 34.21: 1286 34.21 - 51.31: 1119 51.31 - 68.41: 490 68.41 - 85.51: 21 Dihedral angle restraints: 9125 sinusoidal: 6332 harmonic: 2793 Sorted by residual: dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 164.39 15.61 0 5.00e+00 4.00e-02 9.75e+00 dihedral pdb=" CA ARG E 128 " pdb=" CB ARG E 128 " pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -120.60 -59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS D 30 " pdb=" CA LYS D 30 " pdb=" CB LYS D 30 " pdb=" CG LYS D 30 " ideal model delta sinusoidal sigma weight residual -60.00 -117.86 57.86 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 9122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1764 0.029 - 0.058: 581 0.058 - 0.087: 330 0.087 - 0.116: 61 0.116 - 0.146: 8 Chirality restraints: 2744 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE C 111 " pdb=" N ILE C 111 " pdb=" C ILE C 111 " pdb=" CB ILE C 111 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2741 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " 0.024 2.00e-02 2.50e+03 1.20e-02 3.62e+00 pdb=" N1 DT I 88 " -0.027 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 86 " 0.023 2.00e-02 2.50e+03 1.17e-02 3.41e+00 pdb=" N1 DT I 86 " -0.027 2.00e-02 2.50e+03 pdb=" C2 DT I 86 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 86 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 86 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 86 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 86 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 86 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 86 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 86 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO O 238 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " 0.025 5.00e-02 4.00e+02 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1841 2.76 - 3.29: 13546 3.29 - 3.83: 30647 3.83 - 4.36: 36360 4.36 - 4.90: 51294 Nonbonded interactions: 133688 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.219 3.040 nonbonded pdb=" NZ LYS B 91 " pdb=" OE2 GLU H 71 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP B 68 " pdb=" NE2 GLN B 93 " model vdw 2.313 3.120 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.326 3.040 nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.340 3.120 ... (remaining 133683 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 37 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 9 through 119) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 125) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.490 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 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 0.041 16779 Z= 0.197 Angle : 0.632 5.783 24325 Z= 0.397 Chirality : 0.037 0.146 2744 Planarity : 0.004 0.045 1712 Dihedral : 25.723 85.514 7325 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Rotamer: Outliers : 0.25 % Allowed : 1.86 % Favored : 97.89 % 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 aren not related in a simple way. whole: 2.46 (0.27), residues: 945 helix: 2.67 (0.21), residues: 616 sheet: -0.74 (1.27), residues: 20 loop : -0.40 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 208 TYR 0.008 0.001 TYR B 51 PHE 0.007 0.001 PHE A 67 TRP 0.017 0.002 TRP O 214 HIS 0.003 0.001 HIS O 220 Details of bonding type rmsd covalent geometry : bond 0.00450 (16779) covalent geometry : angle 0.63219 (24325) hydrogen bonds : bond 0.10685 ( 957) hydrogen bonds : angle 3.75018 ( 2364) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8675 (tt0) cc_final: 0.8297 (tt0) REVERT: A 123 ASP cc_start: 0.9411 (m-30) cc_final: 0.9151 (m-30) REVERT: D 68 ASP cc_start: 0.9004 (t0) cc_final: 0.8538 (t0) REVERT: D 72 ARG cc_start: 0.9138 (mtt180) cc_final: 0.8812 (mtt180) REVERT: F 59 LYS cc_start: 0.9227 (tttp) cc_final: 0.9014 (tttp) REVERT: G 101 THR cc_start: 0.9178 (t) cc_final: 0.8934 (t) REVERT: H 68 ASP cc_start: 0.9269 (t0) cc_final: 0.8868 (t0) REVERT: H 101 LEU cc_start: 0.9300 (mm) cc_final: 0.9006 (mm) REVERT: H 113 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8593 (mm-30) REVERT: O 201 MET cc_start: 0.6965 (ttt) cc_final: 0.6383 (tmm) REVERT: O 214 TRP cc_start: 0.7558 (p-90) cc_final: 0.7253 (p-90) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.2031 time to fit residues: 50.9732 Evaluate side-chains 167 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.132747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.077950 restraints weight = 27145.151| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.52 r_work: 0.2780 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 16779 Z= 0.369 Angle : 0.627 6.650 24325 Z= 0.372 Chirality : 0.041 0.137 2744 Planarity : 0.005 0.054 1712 Dihedral : 30.166 81.910 5388 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.04 % Rotamer: Outliers : 0.99 % Allowed : 5.45 % Favored : 93.56 % 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 aren not related in a simple way. whole: 2.27 (0.27), residues: 945 helix: 2.50 (0.20), residues: 625 sheet: -0.78 (1.21), residues: 20 loop : -0.50 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 86 TYR 0.012 0.002 TYR H 121 PHE 0.010 0.002 PHE O 204 TRP 0.023 0.002 TRP O 214 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00849 (16779) covalent geometry : angle 0.62739 (24325) hydrogen bonds : bond 0.05192 ( 957) hydrogen bonds : angle 3.04685 ( 2364) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 99 ARG cc_start: 0.8781 (mmm160) cc_final: 0.8561 (mtp85) REVERT: E 73 GLU cc_start: 0.9008 (tt0) cc_final: 0.8741 (tt0) REVERT: F 35 ARG cc_start: 0.8814 (ttm-80) cc_final: 0.8518 (ttp80) REVERT: G 92 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8674 (mm-30) REVERT: H 68 ASP cc_start: 0.9232 (t0) cc_final: 0.8863 (t0) REVERT: H 101 LEU cc_start: 0.9325 (mm) cc_final: 0.8876 (mm) REVERT: H 113 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8653 (mm-30) REVERT: O 201 MET cc_start: 0.6837 (ttt) cc_final: 0.6390 (tmm) REVERT: O 214 TRP cc_start: 0.7217 (p-90) cc_final: 0.6883 (p-90) outliers start: 8 outliers final: 5 residues processed: 171 average time/residue: 0.1980 time to fit residues: 44.9115 Evaluate side-chains 167 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.134983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080672 restraints weight = 27415.452| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.41 r_work: 0.2838 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16779 Z= 0.224 Angle : 0.558 6.191 24325 Z= 0.336 Chirality : 0.034 0.129 2744 Planarity : 0.004 0.056 1712 Dihedral : 29.988 80.692 5388 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.01 % Favored : 97.88 % Rotamer: Outliers : 0.87 % Allowed : 7.06 % Favored : 92.07 % 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 aren not related in a simple way. whole: 2.52 (0.27), residues: 945 helix: 2.70 (0.20), residues: 625 sheet: -0.51 (1.23), residues: 20 loop : -0.44 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.010 0.001 TYR B 51 PHE 0.010 0.001 PHE A 67 TRP 0.020 0.002 TRP O 214 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00505 (16779) covalent geometry : angle 0.55774 (24325) hydrogen bonds : bond 0.04130 ( 957) hydrogen bonds : angle 2.80539 ( 2364) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 73 GLU cc_start: 0.9020 (tt0) cc_final: 0.8766 (tt0) REVERT: E 131 ARG cc_start: 0.9404 (OUTLIER) cc_final: 0.8747 (mtp180) REVERT: F 35 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8485 (ttp80) REVERT: G 101 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9013 (t) REVERT: H 68 ASP cc_start: 0.9231 (t0) cc_final: 0.8852 (t0) REVERT: H 101 LEU cc_start: 0.9337 (mm) cc_final: 0.8907 (mm) REVERT: H 113 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8593 (mm-30) REVERT: O 201 MET cc_start: 0.6895 (ttt) cc_final: 0.6422 (tmm) REVERT: O 214 TRP cc_start: 0.7241 (p-90) cc_final: 0.6896 (p-90) outliers start: 7 outliers final: 5 residues processed: 170 average time/residue: 0.2029 time to fit residues: 45.4369 Evaluate side-chains 174 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 66 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.080247 restraints weight = 27248.946| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.40 r_work: 0.2823 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16779 Z= 0.250 Angle : 0.566 7.055 24325 Z= 0.339 Chirality : 0.035 0.131 2744 Planarity : 0.004 0.058 1712 Dihedral : 30.112 80.232 5388 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 1.24 % Allowed : 7.68 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.27), residues: 945 helix: 2.69 (0.20), residues: 625 sheet: -0.52 (1.22), residues: 20 loop : -0.41 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.010 0.001 TYR G 57 PHE 0.010 0.001 PHE A 67 TRP 0.020 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00569 (16779) covalent geometry : angle 0.56562 (24325) hydrogen bonds : bond 0.04242 ( 957) hydrogen bonds : angle 2.81550 ( 2364) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8972 (tppt) cc_final: 0.8660 (tptt) REVERT: E 73 GLU cc_start: 0.9026 (tt0) cc_final: 0.8781 (tt0) REVERT: E 131 ARG cc_start: 0.9423 (OUTLIER) cc_final: 0.8823 (mtp180) REVERT: F 35 ARG cc_start: 0.8776 (ttm-80) cc_final: 0.8465 (ttp80) REVERT: G 101 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.9051 (t) REVERT: H 68 ASP cc_start: 0.9246 (t0) cc_final: 0.8862 (t0) REVERT: H 86 ARG cc_start: 0.8769 (mmt90) cc_final: 0.8565 (mmt90) REVERT: H 101 LEU cc_start: 0.9361 (mm) cc_final: 0.8918 (mm) REVERT: H 113 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8626 (mm-30) REVERT: O 201 MET cc_start: 0.6901 (ttt) cc_final: 0.6412 (tmm) REVERT: O 214 TRP cc_start: 0.7263 (p-90) cc_final: 0.6936 (p-90) outliers start: 10 outliers final: 6 residues processed: 175 average time/residue: 0.1958 time to fit residues: 45.4182 Evaluate side-chains 173 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.134875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.080704 restraints weight = 27240.209| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.43 r_work: 0.2832 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16779 Z= 0.212 Angle : 0.558 9.136 24325 Z= 0.335 Chirality : 0.034 0.132 2744 Planarity : 0.004 0.059 1712 Dihedral : 30.108 80.480 5388 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.57 % Rotamer: Outliers : 0.99 % Allowed : 8.80 % Favored : 90.21 % 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 aren not related in a simple way. whole: 2.57 (0.27), residues: 945 helix: 2.73 (0.20), residues: 625 sheet: -0.49 (1.19), residues: 20 loop : -0.39 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.010 0.001 TYR B 51 PHE 0.010 0.001 PHE A 67 TRP 0.019 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00477 (16779) covalent geometry : angle 0.55843 (24325) hydrogen bonds : bond 0.04086 ( 957) hydrogen bonds : angle 2.78202 ( 2364) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8988 (tppt) cc_final: 0.8616 (tptt) REVERT: E 73 GLU cc_start: 0.9000 (tt0) cc_final: 0.8748 (tt0) REVERT: E 131 ARG cc_start: 0.9406 (OUTLIER) cc_final: 0.8770 (mtp180) REVERT: F 35 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.8474 (ttp80) REVERT: G 101 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.9056 (t) REVERT: H 68 ASP cc_start: 0.9236 (t0) cc_final: 0.8805 (t0) REVERT: H 101 LEU cc_start: 0.9345 (mm) cc_final: 0.8795 (mm) REVERT: H 113 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8643 (mm-30) REVERT: O 201 MET cc_start: 0.6897 (ttt) cc_final: 0.6413 (tmm) REVERT: O 214 TRP cc_start: 0.7279 (p-90) cc_final: 0.6928 (p-90) outliers start: 8 outliers final: 6 residues processed: 165 average time/residue: 0.1782 time to fit residues: 39.2039 Evaluate side-chains 170 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.136057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.081933 restraints weight = 27265.055| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.39 r_work: 0.2857 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16779 Z= 0.155 Angle : 0.547 10.164 24325 Z= 0.329 Chirality : 0.033 0.133 2744 Planarity : 0.004 0.059 1712 Dihedral : 30.086 80.776 5388 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 0.99 % Allowed : 8.43 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.27), residues: 945 helix: 2.78 (0.20), residues: 625 sheet: -0.46 (1.20), residues: 20 loop : -0.33 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 86 TYR 0.011 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 TRP 0.019 0.002 TRP O 214 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (16779) covalent geometry : angle 0.54701 (24325) hydrogen bonds : bond 0.03819 ( 957) hydrogen bonds : angle 2.74139 ( 2364) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8971 (tppt) cc_final: 0.8689 (tptp) REVERT: E 59 GLU cc_start: 0.9077 (pm20) cc_final: 0.8693 (pm20) REVERT: E 131 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.8752 (mtp180) REVERT: F 35 ARG cc_start: 0.8755 (ttm-80) cc_final: 0.8470 (ttp80) REVERT: G 101 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.9008 (t) REVERT: H 68 ASP cc_start: 0.9185 (t0) cc_final: 0.8773 (t0) REVERT: H 86 ARG cc_start: 0.8721 (mmt90) cc_final: 0.8517 (mmt90) REVERT: H 101 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8810 (mm) REVERT: H 113 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8577 (mm-30) REVERT: O 201 MET cc_start: 0.6892 (ttt) cc_final: 0.6413 (tmm) REVERT: O 214 TRP cc_start: 0.7324 (p-90) cc_final: 0.6951 (p-90) outliers start: 8 outliers final: 4 residues processed: 170 average time/residue: 0.1914 time to fit residues: 43.3333 Evaluate side-chains 170 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 56 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.136817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.082920 restraints weight = 27134.941| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.41 r_work: 0.2882 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16779 Z= 0.162 Angle : 0.534 8.456 24325 Z= 0.323 Chirality : 0.032 0.130 2744 Planarity : 0.004 0.059 1712 Dihedral : 29.894 79.879 5388 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 1.12 % Allowed : 8.43 % Favored : 90.46 % 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 aren not related in a simple way. whole: 2.81 (0.27), residues: 945 helix: 2.90 (0.20), residues: 626 sheet: -0.51 (1.19), residues: 20 loop : -0.30 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 86 TYR 0.009 0.001 TYR A 54 PHE 0.010 0.001 PHE A 67 TRP 0.018 0.002 TRP O 214 HIS 0.003 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00353 (16779) covalent geometry : angle 0.53364 (24325) hydrogen bonds : bond 0.03566 ( 957) hydrogen bonds : angle 2.65934 ( 2364) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8993 (tppt) cc_final: 0.8747 (tptp) REVERT: E 131 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.8594 (mtt180) REVERT: F 35 ARG cc_start: 0.8759 (ttm-80) cc_final: 0.8451 (ttp80) REVERT: F 93 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7983 (mp-120) REVERT: G 101 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9026 (t) REVERT: H 68 ASP cc_start: 0.9162 (t0) cc_final: 0.8789 (t0) REVERT: H 86 ARG cc_start: 0.8704 (mmt90) cc_final: 0.8489 (mmt90) REVERT: H 101 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8843 (mm) REVERT: H 113 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8606 (mm-30) REVERT: O 201 MET cc_start: 0.6927 (ttt) cc_final: 0.6438 (tmm) REVERT: O 214 TRP cc_start: 0.7306 (p-90) cc_final: 0.6949 (p-90) outliers start: 9 outliers final: 5 residues processed: 170 average time/residue: 0.1973 time to fit residues: 44.6042 Evaluate side-chains 174 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 12 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.136097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082079 restraints weight = 27264.952| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.39 r_work: 0.2863 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16779 Z= 0.192 Angle : 0.542 10.225 24325 Z= 0.326 Chirality : 0.033 0.131 2744 Planarity : 0.004 0.060 1712 Dihedral : 29.915 79.604 5388 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 1.49 % Allowed : 8.43 % Favored : 90.09 % 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 aren not related in a simple way. whole: 2.78 (0.27), residues: 945 helix: 2.88 (0.20), residues: 626 sheet: -0.39 (1.20), residues: 20 loop : -0.31 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 86 TYR 0.009 0.001 TYR G 57 PHE 0.009 0.001 PHE A 67 TRP 0.019 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00429 (16779) covalent geometry : angle 0.54179 (24325) hydrogen bonds : bond 0.03718 ( 957) hydrogen bonds : angle 2.68300 ( 2364) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9100 (mtt180) REVERT: C 13 LYS cc_start: 0.8926 (tppt) cc_final: 0.8721 (tptp) REVERT: E 131 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.8699 (mtp180) REVERT: F 35 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8459 (ttp80) REVERT: G 101 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9031 (t) REVERT: H 68 ASP cc_start: 0.9173 (t0) cc_final: 0.8799 (t0) REVERT: H 101 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8842 (mm) REVERT: H 113 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8635 (mm-30) REVERT: O 201 MET cc_start: 0.6894 (ttt) cc_final: 0.6418 (tmm) REVERT: O 214 TRP cc_start: 0.7317 (p-90) cc_final: 0.6957 (p-90) outliers start: 12 outliers final: 7 residues processed: 172 average time/residue: 0.1996 time to fit residues: 45.3412 Evaluate side-chains 174 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.136762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.082914 restraints weight = 27170.227| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.41 r_work: 0.2873 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16779 Z= 0.155 Angle : 0.543 11.244 24325 Z= 0.325 Chirality : 0.032 0.144 2744 Planarity : 0.004 0.059 1712 Dihedral : 29.921 79.920 5388 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 1.24 % Allowed : 9.42 % Favored : 89.34 % 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 aren not related in a simple way. whole: 2.85 (0.27), residues: 945 helix: 2.94 (0.20), residues: 625 sheet: -0.36 (1.20), residues: 20 loop : -0.30 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.010 0.001 TYR D 40 PHE 0.009 0.001 PHE A 67 TRP 0.019 0.002 TRP O 214 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00332 (16779) covalent geometry : angle 0.54266 (24325) hydrogen bonds : bond 0.03612 ( 957) hydrogen bonds : angle 2.67132 ( 2364) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.9099 (mtt180) REVERT: C 13 LYS cc_start: 0.8942 (tppt) cc_final: 0.8728 (tptp) REVERT: E 131 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8685 (mtp180) REVERT: F 35 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8461 (ttp80) REVERT: G 101 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9016 (t) REVERT: H 68 ASP cc_start: 0.9143 (t0) cc_final: 0.8773 (t0) REVERT: H 101 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8856 (mm) REVERT: H 113 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8631 (mm-30) REVERT: O 201 MET cc_start: 0.6904 (ttt) cc_final: 0.6425 (tmm) REVERT: O 214 TRP cc_start: 0.7340 (p-90) cc_final: 0.6964 (p-90) outliers start: 10 outliers final: 6 residues processed: 168 average time/residue: 0.1988 time to fit residues: 44.3464 Evaluate side-chains 169 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 0.0980 chunk 113 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.136973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083214 restraints weight = 27232.548| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.45 r_work: 0.2881 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16779 Z= 0.155 Angle : 0.540 10.947 24325 Z= 0.324 Chirality : 0.032 0.134 2744 Planarity : 0.004 0.059 1712 Dihedral : 29.893 79.954 5388 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 1.12 % Allowed : 9.91 % Favored : 88.97 % 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 aren not related in a simple way. whole: 2.86 (0.27), residues: 945 helix: 2.96 (0.20), residues: 625 sheet: -0.34 (1.19), residues: 20 loop : -0.31 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.010 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 TRP 0.018 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00333 (16779) covalent geometry : angle 0.54014 (24325) hydrogen bonds : bond 0.03537 ( 957) hydrogen bonds : angle 2.65683 ( 2364) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.9122 (mtt180) REVERT: C 13 LYS cc_start: 0.8947 (tppt) cc_final: 0.8727 (tptp) REVERT: E 59 GLU cc_start: 0.9084 (pm20) cc_final: 0.8740 (pm20) REVERT: E 131 ARG cc_start: 0.9379 (OUTLIER) cc_final: 0.8713 (mtt180) REVERT: F 35 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8452 (ttp80) REVERT: G 101 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.9017 (t) REVERT: H 68 ASP cc_start: 0.9136 (t0) cc_final: 0.8774 (t0) REVERT: H 101 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8854 (mm) REVERT: H 113 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8608 (mm-30) REVERT: O 201 MET cc_start: 0.6910 (ttt) cc_final: 0.6428 (tmm) REVERT: O 214 TRP cc_start: 0.7368 (p-90) cc_final: 0.6989 (p-90) outliers start: 9 outliers final: 5 residues processed: 167 average time/residue: 0.2052 time to fit residues: 45.3377 Evaluate side-chains 171 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 121 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.137080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.083365 restraints weight = 27244.704| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.41 r_work: 0.2885 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16779 Z= 0.158 Angle : 0.539 11.081 24325 Z= 0.323 Chirality : 0.032 0.133 2744 Planarity : 0.004 0.059 1712 Dihedral : 29.859 79.908 5388 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 1.12 % Allowed : 10.29 % Favored : 88.60 % 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 aren not related in a simple way. whole: 2.89 (0.27), residues: 945 helix: 2.98 (0.20), residues: 625 sheet: -0.29 (1.20), residues: 20 loop : -0.30 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.009 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 TRP 0.018 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00342 (16779) covalent geometry : angle 0.53938 (24325) hydrogen bonds : bond 0.03501 ( 957) hydrogen bonds : angle 2.64859 ( 2364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5678.12 seconds wall clock time: 97 minutes 16.27 seconds (5836.27 seconds total)