Starting phenix.real_space_refine on Fri Jun 13 18:23:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg2_43198/06_2025/8vg2_43198.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg2_43198/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vg2_43198/06_2025/8vg2_43198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg2_43198/06_2025/8vg2_43198.map" model { file = "/net/cci-nas-00/data/ceres_data/8vg2_43198/06_2025/8vg2_43198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg2_43198/06_2025/8vg2_43198.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.17, per 1000 atoms: 0.58 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: 4.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 7.33 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: 6.48 Time building geometry restraints manager: 4.80 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 41.550 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.000 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.002 TRP O 214 HIS 0.003 0.001 HIS O 220 PHE 0.007 0.001 PHE A 67 TYR 0.008 0.001 TYR B 51 ARG 0.004 0.000 ARG O 208 Details of bonding type rmsd hydrogen bonds : bond 0.10685 ( 957) hydrogen bonds : angle 3.75018 ( 2364) covalent geometry : bond 0.00450 (16779) covalent geometry : angle 0.63219 (24325) *********************** 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 : 1.061 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: 0.3989 time to fit residues: 100.0256 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 : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.134991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.080534 restraints weight = 27178.318| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.44 r_work: 0.2833 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16779 Z= 0.252 Angle : 0.572 6.631 24325 Z= 0.344 Chirality : 0.036 0.131 2744 Planarity : 0.004 0.053 1712 Dihedral : 29.832 81.002 5388 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.57 % Rotamer: Outliers : 0.87 % Allowed : 4.46 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.27), residues: 945 helix: 2.71 (0.21), residues: 625 sheet: -0.72 (1.21), residues: 20 loop : -0.42 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 214 HIS 0.003 0.001 HIS D 49 PHE 0.010 0.001 PHE A 67 TYR 0.009 0.001 TYR B 51 ARG 0.005 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 957) hydrogen bonds : angle 2.89158 ( 2364) covalent geometry : bond 0.00574 (16779) covalent geometry : angle 0.57176 (24325) *********************** 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 174 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9256 (m-30) cc_final: 0.9034 (m-30) REVERT: B 93 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8643 (mm110) REVERT: C 99 ARG cc_start: 0.8774 (mmm160) cc_final: 0.8526 (mtp85) REVERT: E 73 GLU cc_start: 0.8990 (tt0) cc_final: 0.8728 (tt0) REVERT: F 35 ARG cc_start: 0.8819 (ttm-80) cc_final: 0.8525 (ttp80) REVERT: G 92 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8752 (mm-30) REVERT: H 68 ASP cc_start: 0.9164 (t0) cc_final: 0.8809 (t0) REVERT: H 101 LEU cc_start: 0.9312 (mm) cc_final: 0.8931 (mm) REVERT: H 113 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8614 (mm-30) REVERT: O 201 MET cc_start: 0.6835 (ttt) cc_final: 0.6380 (tmm) REVERT: O 214 TRP cc_start: 0.7277 (p-90) cc_final: 0.6915 (p-90) outliers start: 7 outliers final: 5 residues processed: 170 average time/residue: 0.3847 time to fit residues: 87.2032 Evaluate side-chains 166 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 112 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 49 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.136400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.082134 restraints weight = 27094.486| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.42 r_work: 0.2869 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16779 Z= 0.172 Angle : 0.542 7.582 24325 Z= 0.329 Chirality : 0.033 0.130 2744 Planarity : 0.004 0.057 1712 Dihedral : 29.769 81.150 5388 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 0.62 % Allowed : 6.82 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.27), residues: 945 helix: 2.77 (0.20), residues: 626 sheet: -0.78 (1.20), residues: 20 loop : -0.32 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 214 HIS 0.002 0.000 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.005 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 957) hydrogen bonds : angle 2.77343 ( 2364) covalent geometry : bond 0.00376 (16779) covalent geometry : angle 0.54199 (24325) *********************** 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 169 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9210 (m-30) cc_final: 0.8998 (m-30) REVERT: F 35 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8459 (ttp80) REVERT: G 101 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8943 (t) REVERT: H 68 ASP cc_start: 0.9148 (t0) cc_final: 0.8766 (t0) REVERT: H 101 LEU cc_start: 0.9305 (mm) cc_final: 0.8882 (mm) REVERT: H 113 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8552 (mm-30) REVERT: O 201 MET cc_start: 0.6820 (ttt) cc_final: 0.6382 (tmm) REVERT: O 214 TRP cc_start: 0.7246 (p-90) cc_final: 0.6871 (p-90) outliers start: 5 outliers final: 4 residues processed: 166 average time/residue: 0.4117 time to fit residues: 92.3759 Evaluate side-chains 165 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 31 LYS 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 50 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.134107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.079487 restraints weight = 26952.941| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.50 r_work: 0.2811 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16779 Z= 0.284 Angle : 0.576 6.089 24325 Z= 0.346 Chirality : 0.037 0.131 2744 Planarity : 0.004 0.059 1712 Dihedral : 29.986 80.385 5388 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 1.24 % Allowed : 7.19 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.27), residues: 945 helix: 2.68 (0.20), residues: 626 sheet: -0.60 (1.21), residues: 20 loop : -0.37 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 214 HIS 0.003 0.001 HIS D 49 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR D 37 ARG 0.006 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 957) hydrogen bonds : angle 2.86441 ( 2364) covalent geometry : bond 0.00649 (16779) covalent geometry : angle 0.57615 (24325) *********************** 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 178 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9418 (OUTLIER) cc_final: 0.8739 (mtp-110) REVERT: F 35 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8446 (ttp80) REVERT: G 92 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8804 (mm-30) REVERT: H 68 ASP cc_start: 0.9232 (t0) cc_final: 0.8823 (t0) REVERT: H 101 LEU cc_start: 0.9344 (mm) cc_final: 0.8900 (mm) REVERT: H 113 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8614 (mm-30) REVERT: O 201 MET cc_start: 0.6769 (ttt) cc_final: 0.6332 (tmm) REVERT: O 214 TRP cc_start: 0.7209 (p-90) cc_final: 0.6862 (p-90) outliers start: 10 outliers final: 6 residues processed: 173 average time/residue: 0.4654 time to fit residues: 106.8195 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 : 1.175 ------------------------------------------------------------------------------- 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 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 83 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 E 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.135226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.080353 restraints weight = 27373.086| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.54 r_work: 0.2838 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16779 Z= 0.202 Angle : 0.556 8.129 24325 Z= 0.334 Chirality : 0.034 0.133 2744 Planarity : 0.004 0.059 1712 Dihedral : 29.983 80.989 5388 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.22 % Favored : 97.67 % Rotamer: Outliers : 0.62 % Allowed : 8.67 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.27), residues: 945 helix: 2.74 (0.20), residues: 625 sheet: -0.62 (1.20), residues: 20 loop : -0.37 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 214 HIS 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR B 51 ARG 0.008 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 957) hydrogen bonds : angle 2.78326 ( 2364) covalent geometry : bond 0.00451 (16779) covalent geometry : angle 0.55590 (24325) *********************** 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 172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 167 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9067 (m-30) cc_final: 0.8854 (m-30) REVERT: F 35 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.8455 (ttp80) REVERT: G 101 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.9024 (t) REVERT: H 68 ASP cc_start: 0.9182 (t0) cc_final: 0.8797 (t0) REVERT: H 101 LEU cc_start: 0.9334 (mm) cc_final: 0.8912 (mm) REVERT: H 113 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8573 (mm-30) REVERT: O 201 MET cc_start: 0.6776 (ttt) cc_final: 0.6336 (tmm) REVERT: O 214 TRP cc_start: 0.7197 (p-90) cc_final: 0.6835 (p-90) outliers start: 5 outliers final: 4 residues processed: 169 average time/residue: 0.3837 time to fit residues: 86.4113 Evaluate side-chains 170 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 165 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 31 LYS 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 109 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.135789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081559 restraints weight = 27453.118| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.41 r_work: 0.2858 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16779 Z= 0.201 Angle : 0.542 8.215 24325 Z= 0.327 Chirality : 0.033 0.130 2744 Planarity : 0.004 0.060 1712 Dihedral : 29.882 79.653 5388 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 1.24 % Allowed : 7.81 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.27), residues: 945 helix: 2.84 (0.20), residues: 626 sheet: -0.53 (1.22), residues: 20 loop : -0.35 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.009 0.001 TYR G 57 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 957) hydrogen bonds : angle 2.70752 ( 2364) covalent geometry : bond 0.00450 (16779) covalent geometry : angle 0.54154 (24325) *********************** 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 177 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.8702 (mtp180) REVERT: F 35 ARG cc_start: 0.8773 (ttm-80) cc_final: 0.8482 (ttp80) REVERT: G 101 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9034 (t) REVERT: H 68 ASP cc_start: 0.9199 (t0) cc_final: 0.8832 (t0) REVERT: H 101 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8919 (mm) REVERT: H 113 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8591 (mm-30) REVERT: O 201 MET cc_start: 0.6911 (ttt) cc_final: 0.6422 (tmm) REVERT: O 214 TRP cc_start: 0.7262 (p-90) cc_final: 0.6925 (p-90) outliers start: 10 outliers final: 6 residues processed: 173 average time/residue: 0.3952 time to fit residues: 91.5164 Evaluate side-chains 172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 G residue 76 THR 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 16 optimal weight: 0.4980 chunk 125 optimal weight: 9.9990 chunk 115 optimal weight: 0.0050 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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** B 93 GLN C 73 ASN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.136850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.082758 restraints weight = 27294.968| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.39 r_work: 0.2880 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1470 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= 0.148 Angle : 0.535 10.140 24325 Z= 0.323 Chirality : 0.032 0.133 2744 Planarity : 0.004 0.060 1712 Dihedral : 29.885 79.996 5388 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.22 % Favored : 97.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.27), residues: 945 helix: 2.88 (0.20), residues: 626 sheet: -0.51 (1.21), residues: 20 loop : -0.31 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 214 HIS 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.011 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 957) hydrogen bonds : angle 2.67541 ( 2364) covalent geometry : bond 0.00313 (16779) covalent geometry : angle 0.53505 (24325) *********************** 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 171 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.9104 (pm20) cc_final: 0.8745 (pm20) REVERT: E 131 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.8625 (mtp-110) REVERT: F 35 ARG cc_start: 0.8743 (ttm-80) cc_final: 0.8456 (ttp80) REVERT: G 101 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.8995 (t) REVERT: H 68 ASP cc_start: 0.9123 (t0) cc_final: 0.8773 (t0) REVERT: H 101 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8925 (mm) REVERT: H 113 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8580 (mm-30) REVERT: O 201 MET cc_start: 0.6900 (ttt) cc_final: 0.6420 (tmm) REVERT: O 214 TRP cc_start: 0.7258 (p-90) cc_final: 0.6905 (p-90) outliers start: 8 outliers final: 5 residues processed: 168 average time/residue: 0.4521 time to fit residues: 102.4682 Evaluate side-chains 168 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- 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** B 93 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.137326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.083609 restraints weight = 27193.261| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.41 r_work: 0.2892 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16779 Z= 0.158 Angle : 0.537 9.736 24325 Z= 0.323 Chirality : 0.032 0.130 2744 Planarity : 0.004 0.059 1712 Dihedral : 29.784 79.689 5388 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 0.62 % Allowed : 9.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.27), residues: 945 helix: 2.94 (0.20), residues: 626 sheet: -0.46 (1.21), residues: 20 loop : -0.29 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 214 HIS 0.003 0.000 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.011 0.001 TYR A 54 ARG 0.008 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 957) hydrogen bonds : angle 2.63431 ( 2364) covalent geometry : bond 0.00343 (16779) covalent geometry : angle 0.53661 (24325) *********************** 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 173 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8622 (tppt) cc_final: 0.8164 (tptt) REVERT: E 59 GLU cc_start: 0.9115 (pm20) cc_final: 0.8732 (pm20) REVERT: F 35 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.8445 (ttp80) REVERT: G 101 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9037 (t) REVERT: H 68 ASP cc_start: 0.9137 (t0) cc_final: 0.8830 (t0) REVERT: H 101 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8815 (mm) REVERT: H 113 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8608 (mm-30) REVERT: O 201 MET cc_start: 0.6886 (ttt) cc_final: 0.6409 (tmm) REVERT: O 214 TRP cc_start: 0.7263 (p-90) cc_final: 0.6916 (p-90) outliers start: 5 outliers final: 3 residues processed: 170 average time/residue: 0.4226 time to fit residues: 95.8757 Evaluate side-chains 168 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 114 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** B 93 GLN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.134230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.079914 restraints weight = 27191.116| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.48 r_work: 0.2801 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16779 Z= 0.283 Angle : 0.585 9.937 24325 Z= 0.347 Chirality : 0.037 0.133 2744 Planarity : 0.004 0.060 1712 Dihedral : 30.114 80.178 5388 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 1.12 % Allowed : 9.42 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.27), residues: 945 helix: 2.79 (0.20), residues: 625 sheet: -0.40 (1.20), residues: 20 loop : -0.40 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 214 HIS 0.003 0.001 HIS G 31 PHE 0.007 0.001 PHE A 67 TYR 0.009 0.001 TYR G 57 ARG 0.010 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 957) hydrogen bonds : angle 2.80250 ( 2364) covalent geometry : bond 0.00646 (16779) covalent geometry : angle 0.58462 (24325) *********************** 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 174 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8792 (tppt) cc_final: 0.8282 (tptt) REVERT: E 131 ARG cc_start: 0.9407 (OUTLIER) cc_final: 0.8760 (mtp180) REVERT: F 35 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8464 (ttp80) REVERT: H 68 ASP cc_start: 0.9232 (t0) cc_final: 0.8835 (t0) REVERT: H 101 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8918 (mm) REVERT: H 113 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8636 (mm-30) REVERT: O 201 MET cc_start: 0.6855 (ttt) cc_final: 0.6346 (tmm) REVERT: O 214 TRP cc_start: 0.7195 (p-90) cc_final: 0.6820 (p-90) outliers start: 9 outliers final: 7 residues processed: 170 average time/residue: 0.4219 time to fit residues: 96.2194 Evaluate side-chains 173 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** B 93 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.080149 restraints weight = 27624.083| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.44 r_work: 0.2797 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16779 Z= 0.160 Angle : 0.557 10.720 24325 Z= 0.334 Chirality : 0.033 0.131 2744 Planarity : 0.004 0.059 1712 Dihedral : 30.124 80.847 5388 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.57 % Rotamer: Outliers : 0.74 % Allowed : 9.79 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.27), residues: 945 helix: 2.80 (0.20), residues: 625 sheet: -0.40 (1.21), residues: 20 loop : -0.38 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.013 0.001 TYR B 51 ARG 0.010 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 957) hydrogen bonds : angle 2.71247 ( 2364) covalent geometry : bond 0.00344 (16779) covalent geometry : angle 0.55700 (24325) ********************** 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: 6 poor density : 165 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8780 (tppt) cc_final: 0.8295 (tptt) REVERT: F 35 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8493 (ttp80) REVERT: G 101 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9058 (t) REVERT: H 68 ASP cc_start: 0.9242 (t0) cc_final: 0.8792 (t0) REVERT: H 101 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8919 (mm) REVERT: H 113 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8604 (mm-30) REVERT: O 201 MET cc_start: 0.6890 (ttt) cc_final: 0.6401 (tmm) REVERT: O 214 TRP cc_start: 0.7133 (p-90) cc_final: 0.6772 (p-90) outliers start: 6 outliers final: 4 residues processed: 168 average time/residue: 0.3974 time to fit residues: 88.7849 Evaluate side-chains 168 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 0.0980 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** B 93 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.133762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.079801 restraints weight = 27697.078| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.51 r_work: 0.2793 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16779 Z= 0.206 Angle : 0.557 10.809 24325 Z= 0.333 Chirality : 0.033 0.131 2744 Planarity : 0.004 0.060 1712 Dihedral : 29.972 79.820 5388 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.04 % Rotamer: Outliers : 0.87 % Allowed : 9.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.27), residues: 945 helix: 2.87 (0.20), residues: 625 sheet: -0.34 (1.22), residues: 20 loop : -0.41 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 214 HIS 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.013 0.001 TYR B 88 ARG 0.009 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 957) hydrogen bonds : angle 2.70489 ( 2364) covalent geometry : bond 0.00463 (16779) covalent geometry : angle 0.55720 (24325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11474.37 seconds wall clock time: 202 minutes 11.59 seconds (12131.59 seconds total)