Starting phenix.real_space_refine on Tue Feb 11 06:52:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rtb_4996/02_2025/6rtb_4996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rtb_4996/02_2025/6rtb_4996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rtb_4996/02_2025/6rtb_4996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rtb_4996/02_2025/6rtb_4996.map" model { file = "/net/cci-nas-00/data/ceres_data/6rtb_4996/02_2025/6rtb_4996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rtb_4996/02_2025/6rtb_4996.cif" } resolution = 3.46 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: 3 Type Number sf(0) Gaussians C 2895 2.51 5 N 829 2.21 5 O 957 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-5592/modules/chem_data/mon_lib" Total number of atoms: 4681 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "I" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 460 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain breaks: 2 Chain: "J" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "E" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "G" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "B" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "F" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "A" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Time building chain proxies: 3.51, per 1000 atoms: 0.75 Number of scatterers: 4681 At special positions: 0 Unit cell: (104.24, 132.431, 41.9584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 957 8.00 N 829 7.00 C 2895 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: 1.13 Conformation dependent library (CDL) restraints added in 616.8 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 15 through 17 removed outlier: 6.428A pdb=" N VAL H 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 37 through 43 removed outlier: 6.129A pdb=" N GLY I 36 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N TYR J 39 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU I 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY J 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL I 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS J 43 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER I 42 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL G 37 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL F 40 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR G 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N SER F 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY G 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.537A pdb=" N VAL H 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL G 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 65 through 66 removed outlier: 6.779A pdb=" N ASN H 65 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN G 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 70 through 72 removed outlier: 6.593A pdb=" N VAL G 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 75 through 79 removed outlier: 6.403A pdb=" N ALA H 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLN G 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA H 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA G 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN F 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA G 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 82 through 83 removed outlier: 6.722A pdb=" N VAL H 82 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL G 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 89 through 91 removed outlier: 6.262A pdb=" N ALA H 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA I 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.424A pdb=" N VAL C 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 15 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 37 through 43 removed outlier: 6.463A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY E 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LYS E 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER D 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY D 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL C 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS D 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 47 through 52 removed outlier: 6.859A pdb=" N VAL E 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL D 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL C 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLY B 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N HIS C 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 48 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLY A 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N HIS B 50 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.196A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 75 through 79 removed outlier: 6.346A pdb=" N THR D 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA E 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL D 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR C 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA D 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 88 through 89 removed outlier: 6.494A pdb=" N SER C 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 89 through 90 79 hydrogen bonds defined for protein. 237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 837 1.29 - 1.35: 733 1.35 - 1.42: 127 1.42 - 1.49: 864 1.49 - 1.56: 2110 Bond restraints: 4671 Sorted by residual: bond pdb=" CB VAL G 16 " pdb=" CG2 VAL G 16 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.57e+00 bond pdb=" N ALA C 19 " pdb=" CA ALA C 19 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.59e+00 bond pdb=" CA THR D 92 " pdb=" CB THR D 92 " ideal model delta sigma weight residual 1.534 1.497 0.037 1.78e-02 3.16e+03 4.32e+00 bond pdb=" N ALA B 19 " pdb=" CA ALA B 19 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.29e+00 bond pdb=" CB VAL F 16 " pdb=" CG1 VAL F 16 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.16e+00 ... (remaining 4666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 5645 1.86 - 3.72: 527 3.72 - 5.59: 86 5.59 - 7.45: 25 7.45 - 9.31: 5 Bond angle restraints: 6288 Sorted by residual: angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 112.96 104.63 8.33 1.00e+00 1.00e+00 6.94e+01 angle pdb=" CG1 VAL G 16 " pdb=" CB VAL G 16 " pdb=" CG2 VAL G 16 " ideal model delta sigma weight residual 110.80 101.49 9.31 2.20e+00 2.07e-01 1.79e+01 angle pdb=" CG1 VAL H 16 " pdb=" CB VAL H 16 " pdb=" CG2 VAL H 16 " ideal model delta sigma weight residual 110.80 101.54 9.26 2.20e+00 2.07e-01 1.77e+01 angle pdb=" C ALA F 18 " pdb=" N ALA F 19 " pdb=" CA ALA F 19 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C ALA C 18 " pdb=" N ALA C 19 " pdb=" CA ALA C 19 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 ... (remaining 6283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2404 16.64 - 33.29: 265 33.29 - 49.93: 50 49.93 - 66.58: 8 66.58 - 83.22: 7 Dihedral angle restraints: 2734 sinusoidal: 877 harmonic: 1857 Sorted by residual: dihedral pdb=" CA ALA G 19 " pdb=" C ALA G 19 " pdb=" N GLU G 20 " pdb=" CA GLU G 20 " ideal model delta harmonic sigma weight residual 180.00 113.95 66.05 0 5.00e+00 4.00e-02 1.74e+02 dihedral pdb=" CA ALA C 19 " pdb=" C ALA C 19 " pdb=" N GLU C 20 " pdb=" CA GLU C 20 " ideal model delta harmonic sigma weight residual 180.00 128.01 51.99 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA ALA I 19 " pdb=" C ALA I 19 " pdb=" N GLU I 20 " pdb=" CA GLU I 20 " ideal model delta harmonic sigma weight residual 180.00 128.78 51.22 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 2731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 494 0.057 - 0.115: 260 0.115 - 0.172: 68 0.172 - 0.230: 10 0.230 - 0.287: 7 Chirality restraints: 839 Sorted by residual: chirality pdb=" CB THR I 81 " pdb=" CA THR I 81 " pdb=" OG1 THR I 81 " pdb=" CG2 THR I 81 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB THR B 92 " pdb=" CA THR B 92 " pdb=" OG1 THR B 92 " pdb=" CG2 THR B 92 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR D 92 " pdb=" CA THR D 92 " pdb=" OG1 THR D 92 " pdb=" CG2 THR D 92 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 836 not shown) Planarity restraints: 778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 18 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C ALA G 18 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA G 18 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA G 19 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 19 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C ALA J 19 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA J 19 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU J 20 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 18 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C ALA F 18 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA F 18 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA F 19 " 0.013 2.00e-02 2.50e+03 ... (remaining 775 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 141 2.68 - 3.23: 3871 3.23 - 3.79: 6452 3.79 - 4.34: 8026 4.34 - 4.90: 15387 Nonbonded interactions: 33877 Sorted by model distance: nonbonded pdb=" OG SER G 87 " pdb=" O ALA F 18 " model vdw 2.122 3.040 nonbonded pdb=" O SER E 9 " pdb=" OG SER E 9 " model vdw 2.294 3.040 nonbonded pdb=" O SER C 9 " pdb=" OG SER C 9 " model vdw 2.297 3.040 nonbonded pdb=" O SER B 9 " pdb=" OG SER B 9 " model vdw 2.299 3.040 nonbonded pdb=" O SER D 9 " pdb=" OG SER D 9 " model vdw 2.301 3.040 ... (remaining 33872 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 9 through 24 or resid 36 through 93)) selection = (chain 'B' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'C' and (resid 9 through 24 or resid 36 through 93)) selection = chain 'D' selection = (chain 'E' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'F' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'G' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'H' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'I' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'J' and (resid 9 through 24 or resid 36 through 93)) } 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: 1.060 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.460 Find NCS groups from input model: 0.280 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.009 0.078 4671 Z= 0.610 Angle : 1.226 9.311 6288 Z= 0.718 Chirality : 0.072 0.287 839 Planarity : 0.005 0.025 778 Dihedral : 15.078 83.221 1556 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 18.94 % Favored : 80.91 % Rotamer: Outliers : 2.61 % Allowed : 11.33 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.94 % 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: -4.64 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 50 TYR 0.028 0.005 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: H 13 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6179 (mp0) REVERT: C 43 LYS cc_start: 0.8320 (tttt) cc_final: 0.8085 (tttp) REVERT: I 13 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6740 (tt0) REVERT: D 43 LYS cc_start: 0.8128 (tttt) cc_final: 0.7667 (mptt) REVERT: D 80 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8183 (ttmt) REVERT: J 12 LYS cc_start: 0.7253 (mttt) cc_final: 0.5327 (tmtt) REVERT: J 13 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7571 (tt0) REVERT: J 46 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7883 (tm-30) REVERT: J 83 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7619 (mp0) REVERT: G 13 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6421 (mp0) REVERT: B 43 LYS cc_start: 0.8343 (tttt) cc_final: 0.8125 (tttp) REVERT: B 80 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8200 (ttmt) REVERT: F 13 GLU cc_start: 0.6671 (mt-10) cc_final: 0.5959 (tt0) REVERT: F 24 GLN cc_start: 0.7623 (mt0) cc_final: 0.7284 (tm-30) REVERT: F 83 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6867 (mt-10) REVERT: A 80 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8310 (ttmt) outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.2012 time to fit residues: 25.5867 Evaluate side-chains 91 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain A residue 15 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 ASN C 50 HIS C 62 GLN C 79 GLN I 62 GLN I 79 GLN D 79 GLN J 62 GLN E 79 GLN G 62 GLN B 50 HIS B 62 GLN B 79 GLN F 62 GLN A 50 HIS A 62 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.158670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.137511 restraints weight = 6871.972| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.41 r_work: 0.4102 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3963 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4671 Z= 0.245 Angle : 0.738 5.937 6288 Z= 0.413 Chirality : 0.052 0.140 839 Planarity : 0.002 0.015 778 Dihedral : 9.286 49.418 687 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.12 % Favored : 83.88 % Rotamer: Outliers : 6.97 % Allowed : 10.68 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.20 % 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: -4.39 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 TYR 0.014 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.495 Fit side-chains REVERT: H 13 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6297 (mp0) REVERT: C 80 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7931 (ttmt) REVERT: C 92 THR cc_start: 0.7866 (p) cc_final: 0.7457 (p) REVERT: I 13 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6769 (tt0) REVERT: D 43 LYS cc_start: 0.8387 (tttt) cc_final: 0.7684 (mptt) REVERT: D 80 LYS cc_start: 0.8603 (mtpt) cc_final: 0.7998 (mttp) REVERT: D 92 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7886 (p) REVERT: J 12 LYS cc_start: 0.7344 (mttt) cc_final: 0.5774 (tmtt) REVERT: J 13 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7448 (tt0) REVERT: J 46 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8194 (tm-30) REVERT: J 81 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7462 (p) REVERT: J 83 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7822 (mp0) REVERT: G 13 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6245 (mp0) REVERT: B 80 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8026 (mttp) REVERT: F 13 GLU cc_start: 0.6611 (mt-10) cc_final: 0.5875 (mm-30) REVERT: F 24 GLN cc_start: 0.7535 (mt0) cc_final: 0.7105 (tm-30) REVERT: F 83 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7044 (mt-10) REVERT: A 80 LYS cc_start: 0.8447 (mtpt) cc_final: 0.7901 (ttmt) outliers start: 32 outliers final: 15 residues processed: 103 average time/residue: 0.1625 time to fit residues: 21.3269 Evaluate side-chains 88 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain A residue 15 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 0.0000 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 0.0020 chunk 6 optimal weight: 3.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN I 62 GLN D 50 HIS J 62 GLN G 62 GLN B 62 GLN F 62 GLN A 62 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.156015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.134585 restraints weight = 7065.489| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.50 r_work: 0.4100 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4671 Z= 0.359 Angle : 0.767 5.428 6288 Z= 0.433 Chirality : 0.053 0.196 839 Planarity : 0.003 0.011 778 Dihedral : 9.130 44.030 687 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.94 % Favored : 81.06 % Rotamer: Outliers : 8.28 % Allowed : 12.85 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -4.77 (0.29), residues: 639 helix: None (None), residues: 0 sheet: -3.54 (0.47), residues: 117 loop : -3.40 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 TYR 0.018 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 72 time to evaluate : 0.481 Fit side-chains REVERT: H 13 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6412 (mp0) REVERT: C 92 THR cc_start: 0.7875 (p) cc_final: 0.7485 (p) REVERT: I 13 GLU cc_start: 0.7558 (mt-10) cc_final: 0.6883 (tt0) REVERT: D 43 LYS cc_start: 0.8351 (tttt) cc_final: 0.7704 (mptt) REVERT: D 80 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8139 (mttp) REVERT: D 92 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7839 (p) REVERT: J 12 LYS cc_start: 0.7261 (mttt) cc_final: 0.5614 (tmtt) REVERT: J 13 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7541 (tt0) REVERT: J 81 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7273 (p) REVERT: J 83 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7704 (mp0) REVERT: G 13 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6501 (mp0) REVERT: G 24 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7831 (tm-30) REVERT: B 80 LYS cc_start: 0.8360 (mtpt) cc_final: 0.8060 (mtmt) REVERT: F 13 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6141 (tt0) REVERT: F 24 GLN cc_start: 0.7466 (mt0) cc_final: 0.7211 (tm-30) REVERT: F 83 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6940 (mt-10) REVERT: A 80 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8183 (mtpp) outliers start: 38 outliers final: 24 residues processed: 102 average time/residue: 0.1502 time to fit residues: 19.9290 Evaluate side-chains 96 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 15 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.0020 chunk 62 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 0 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN I 62 GLN J 62 GLN G 62 GLN B 62 GLN F 62 GLN A 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.164359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.141457 restraints weight = 6739.257| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.59 r_work: 0.4182 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4671 Z= 0.158 Angle : 0.642 5.757 6288 Z= 0.357 Chirality : 0.051 0.141 839 Planarity : 0.002 0.007 778 Dihedral : 7.579 37.775 687 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 6.10 % Allowed : 15.47 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.14 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 TYR 0.008 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.469 Fit side-chains REVERT: H 13 GLU cc_start: 0.6325 (mt-10) cc_final: 0.5840 (tt0) REVERT: C 43 LYS cc_start: 0.8194 (tttt) cc_final: 0.7477 (mptt) REVERT: C 80 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7776 (mtmt) REVERT: C 92 THR cc_start: 0.7826 (p) cc_final: 0.7437 (p) REVERT: I 13 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6512 (tt0) REVERT: D 43 LYS cc_start: 0.8159 (tttt) cc_final: 0.7517 (mptt) REVERT: D 80 LYS cc_start: 0.8405 (mtpt) cc_final: 0.7941 (mttp) REVERT: D 92 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7678 (p) REVERT: J 13 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7289 (tt0) REVERT: J 83 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7502 (mp0) REVERT: G 13 GLU cc_start: 0.6354 (mt-10) cc_final: 0.6127 (mp0) REVERT: B 80 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7761 (mtmt) REVERT: F 24 GLN cc_start: 0.7440 (mt0) cc_final: 0.7127 (tm-30) REVERT: F 83 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7071 (mt-10) REVERT: A 83 GLU cc_start: 0.7516 (mp0) cc_final: 0.7187 (mp0) outliers start: 28 outliers final: 15 residues processed: 99 average time/residue: 0.1546 time to fit residues: 19.6720 Evaluate side-chains 84 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 34 optimal weight: 0.0770 chunk 15 optimal weight: 9.9990 chunk 36 optimal weight: 0.0270 chunk 35 optimal weight: 7.9990 chunk 39 optimal weight: 0.3980 chunk 42 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN I 62 GLN J 62 GLN G 62 GLN B 62 GLN F 62 GLN A 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.168310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.145064 restraints weight = 6767.324| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 2.64 r_work: 0.4238 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4671 Z= 0.149 Angle : 0.579 5.616 6288 Z= 0.322 Chirality : 0.050 0.133 839 Planarity : 0.001 0.009 778 Dihedral : 6.709 36.220 685 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.18 % Favored : 84.82 % Rotamer: Outliers : 6.54 % Allowed : 15.03 % Favored : 78.43 % 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: -3.96 (0.29), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 TYR 0.008 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.469 Fit side-chains REVERT: H 13 GLU cc_start: 0.6200 (mt-10) cc_final: 0.5584 (mp0) REVERT: C 80 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7735 (mtmt) REVERT: C 92 THR cc_start: 0.7786 (p) cc_final: 0.7405 (p) REVERT: I 13 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6595 (tt0) REVERT: D 80 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7935 (mttp) REVERT: D 92 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7634 (p) REVERT: J 13 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7252 (tt0) REVERT: J 83 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7638 (mp0) REVERT: E 43 LYS cc_start: 0.7882 (tttt) cc_final: 0.6727 (mptt) REVERT: G 13 GLU cc_start: 0.6281 (mt-10) cc_final: 0.6062 (mp0) REVERT: B 80 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7753 (mtmt) REVERT: F 24 GLN cc_start: 0.7477 (mt0) cc_final: 0.7112 (tm-30) REVERT: F 83 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7063 (mt-10) outliers start: 30 outliers final: 18 residues processed: 97 average time/residue: 0.1582 time to fit residues: 19.6480 Evaluate side-chains 83 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain A residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN H 65 ASN C 62 GLN I 62 GLN J 62 GLN E 50 HIS G 62 GLN B 62 GLN F 62 GLN A 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.157025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.135592 restraints weight = 7101.893| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.45 r_work: 0.4083 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3944 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 4671 Z= 0.449 Angle : 0.778 5.445 6288 Z= 0.440 Chirality : 0.054 0.139 839 Planarity : 0.003 0.013 778 Dihedral : 8.375 39.086 685 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.41 % Favored : 80.59 % Rotamer: Outliers : 7.84 % Allowed : 15.25 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -4.18 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 TYR 0.023 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 64 time to evaluate : 0.498 Fit side-chains REVERT: H 13 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6449 (mp0) REVERT: H 24 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7675 (tm-30) REVERT: H 46 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.6818 (tm-30) REVERT: C 92 THR cc_start: 0.8139 (p) cc_final: 0.7818 (p) REVERT: I 13 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6807 (tt0) REVERT: D 80 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8119 (mttp) REVERT: J 12 LYS cc_start: 0.7489 (mttt) cc_final: 0.5944 (tmtt) REVERT: J 13 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7537 (tt0) REVERT: J 83 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7843 (mp0) REVERT: G 13 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6455 (mp0) REVERT: G 24 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7555 (tm-30) REVERT: G 46 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: B 80 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7925 (ttmt) REVERT: F 24 GLN cc_start: 0.7567 (mt0) cc_final: 0.7134 (tm-30) REVERT: F 83 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7009 (mt-10) outliers start: 36 outliers final: 27 residues processed: 94 average time/residue: 0.1417 time to fit residues: 17.6441 Evaluate side-chains 92 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 0.0270 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN I 62 GLN J 62 GLN G 62 GLN B 62 GLN F 62 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.157604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.134768 restraints weight = 6843.116| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.63 r_work: 0.4096 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4671 Z= 0.292 Angle : 0.702 5.311 6288 Z= 0.396 Chirality : 0.053 0.182 839 Planarity : 0.002 0.010 778 Dihedral : 8.014 39.071 685 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.59 % Favored : 83.41 % Rotamer: Outliers : 7.41 % Allowed : 15.90 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.19 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 TYR 0.015 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.511 Fit side-chains REVERT: H 13 GLU cc_start: 0.6643 (mt-10) cc_final: 0.5933 (mp0) REVERT: H 24 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7541 (tm-30) REVERT: H 83 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7394 (mp0) REVERT: I 13 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6689 (tt0) REVERT: D 80 LYS cc_start: 0.8372 (mtpt) cc_final: 0.8071 (mttp) REVERT: J 12 LYS cc_start: 0.7339 (mttt) cc_final: 0.5777 (tmtt) REVERT: J 13 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7524 (tt0) REVERT: J 83 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7724 (mp0) REVERT: G 13 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6257 (tt0) REVERT: G 24 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7581 (tm-30) REVERT: G 46 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: B 80 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7843 (mttp) REVERT: F 24 GLN cc_start: 0.7572 (mt0) cc_final: 0.7138 (tm-30) REVERT: F 83 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6979 (mt-10) REVERT: A 83 GLU cc_start: 0.7935 (mp0) cc_final: 0.7533 (mp0) outliers start: 34 outliers final: 23 residues processed: 92 average time/residue: 0.1314 time to fit residues: 16.1725 Evaluate side-chains 86 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 62 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN I 62 GLN G 62 GLN B 62 GLN F 62 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.154577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.132446 restraints weight = 7027.195| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.51 r_work: 0.4031 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 4671 Z= 0.479 Angle : 0.822 5.066 6288 Z= 0.467 Chirality : 0.056 0.164 839 Planarity : 0.003 0.010 778 Dihedral : 8.708 39.624 685 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.00 % Favored : 77.00 % Rotamer: Outliers : 7.63 % Allowed : 15.69 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -4.51 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 50 TYR 0.022 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 0.485 Fit side-chains REVERT: H 13 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6359 (mp0) REVERT: H 24 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7548 (tm-30) REVERT: H 46 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: I 13 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6678 (tt0) REVERT: D 80 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8158 (mttp) REVERT: J 12 LYS cc_start: 0.7497 (mttt) cc_final: 0.5916 (tmtt) REVERT: J 13 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7464 (tt0) REVERT: J 83 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7810 (mp0) REVERT: G 13 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6514 (mp0) REVERT: G 24 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7563 (tm-30) REVERT: G 46 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: B 80 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7811 (mttp) REVERT: F 24 GLN cc_start: 0.7656 (mt0) cc_final: 0.7178 (tm-30) REVERT: F 83 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6973 (mt-10) outliers start: 35 outliers final: 28 residues processed: 91 average time/residue: 0.1367 time to fit residues: 16.6044 Evaluate side-chains 92 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN I 62 GLN G 62 GLN B 62 GLN F 62 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.156608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.133609 restraints weight = 6944.971| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.67 r_work: 0.4086 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4671 Z= 0.280 Angle : 0.727 5.412 6288 Z= 0.408 Chirality : 0.053 0.143 839 Planarity : 0.002 0.010 778 Dihedral : 8.102 39.193 684 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.59 % Favored : 83.41 % Rotamer: Outliers : 6.75 % Allowed : 16.78 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.33 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 TYR 0.014 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.523 Fit side-chains REVERT: H 13 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6066 (tt0) REVERT: H 24 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7490 (tm-30) REVERT: H 46 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: H 83 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7452 (mp0) REVERT: C 80 LYS cc_start: 0.8364 (mtpt) cc_final: 0.7850 (mtmt) REVERT: I 13 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6571 (tt0) REVERT: D 80 LYS cc_start: 0.8380 (mtpt) cc_final: 0.8054 (mttp) REVERT: J 12 LYS cc_start: 0.7352 (mttt) cc_final: 0.5832 (tmtt) REVERT: J 13 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7496 (tt0) REVERT: J 83 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7697 (mp0) REVERT: G 13 GLU cc_start: 0.6627 (mt-10) cc_final: 0.6194 (tt0) REVERT: G 24 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7599 (tm-30) REVERT: G 46 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.6671 (tm-30) REVERT: B 80 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7857 (mttp) REVERT: F 24 GLN cc_start: 0.7593 (mt0) cc_final: 0.7149 (tm-30) REVERT: F 83 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7028 (mt-10) REVERT: A 83 GLU cc_start: 0.7909 (mp0) cc_final: 0.7475 (mp0) outliers start: 31 outliers final: 24 residues processed: 88 average time/residue: 0.1368 time to fit residues: 16.0686 Evaluate side-chains 88 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain A residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 65 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN I 62 GLN G 62 GLN B 62 GLN F 62 GLN F 65 ASN A 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.164898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.142875 restraints weight = 6795.273| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.44 r_work: 0.4210 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4671 Z= 0.181 Angle : 0.675 7.083 6288 Z= 0.373 Chirality : 0.051 0.141 839 Planarity : 0.002 0.013 778 Dihedral : 7.189 38.875 684 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.43 % Favored : 83.57 % Rotamer: Outliers : 5.45 % Allowed : 17.65 % Favored : 76.91 % 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: -4.05 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 50 TYR 0.008 0.002 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.510 Fit side-chains REVERT: H 13 GLU cc_start: 0.6407 (mt-10) cc_final: 0.5949 (tt0) REVERT: H 46 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: H 83 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7676 (mp0) REVERT: C 80 LYS cc_start: 0.8375 (mtpt) cc_final: 0.7857 (mtmt) REVERT: I 13 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6467 (tt0) REVERT: D 80 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8025 (mttp) REVERT: J 12 LYS cc_start: 0.7205 (mttt) cc_final: 0.5652 (tmtt) REVERT: J 13 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7332 (tt0) REVERT: J 83 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7694 (mp0) REVERT: G 13 GLU cc_start: 0.6476 (mt-10) cc_final: 0.6131 (tt0) REVERT: B 80 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7925 (mttp) REVERT: F 24 GLN cc_start: 0.7539 (mt0) cc_final: 0.7111 (tm-30) REVERT: F 83 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7264 (mt-10) REVERT: A 83 GLU cc_start: 0.7877 (mp0) cc_final: 0.7553 (mp0) outliers start: 25 outliers final: 21 residues processed: 85 average time/residue: 0.1360 time to fit residues: 15.5927 Evaluate side-chains 85 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain A residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 0.0030 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 0.1980 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 59 optimal weight: 0.2980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN I 62 GLN G 62 GLN B 62 GLN A 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.165429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.143381 restraints weight = 6796.547| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 2.41 r_work: 0.4211 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.234 4671 Z= 0.695 Angle : 1.863 59.197 6288 Z= 1.138 Chirality : 0.069 0.935 839 Planarity : 0.007 0.171 778 Dihedral : 7.185 38.891 684 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.28 % Favored : 83.72 % Rotamer: Outliers : 5.45 % Allowed : 17.65 % Favored : 76.91 % Cbeta Deviations : 0.68 % 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: -4.03 (0.29), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 50 TYR 0.008 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.52 seconds wall clock time: 42 minutes 29.59 seconds (2549.59 seconds total)