Starting phenix.real_space_refine on Thu Mar 6 02:39:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rtb_4996/03_2025/6rtb_4996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rtb_4996/03_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_4996/03_2025/6rtb_4996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rtb_4996/03_2025/6rtb_4996.map" model { file = "/net/cci-nas-00/data/ceres_data/6rtb_4996/03_2025/6rtb_4996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rtb_4996/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.45, per 1000 atoms: 0.74 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: 0.99 Conformation dependent library (CDL) restraints added in 639.7 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: 0.77 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: 1.15 Time building geometry restraints manager: 1.19 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.930 Find NCS groups from input model: 0.260 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.560 ------------------------------------------------------------------------------- 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 : 0.708 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: 0.1980 time to fit residues: 25.3876 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 : 0.469 ------------------------------------------------------------------------------- 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: 0.3962 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 0.643 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: 0.7868 (p) cc_final: 0.7458 (p) REVERT: I 13 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6769 (tt0) REVERT: D 43 LYS cc_start: 0.8388 (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: 0.8178 (OUTLIER) cc_final: 0.7887 (p) REVERT: J 12 LYS cc_start: 0.7344 (mttt) cc_final: 0.5775 (tmtt) REVERT: J 13 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7448 (tt0) REVERT: J 46 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8193 (tm-30) REVERT: J 81 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7463 (p) REVERT: J 83 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7822 (mp0) REVERT: G 13 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6243 (mp0) REVERT: B 80 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8027 (mttp) REVERT: F 13 GLU cc_start: 0.6611 (mt-10) cc_final: 0.5874 (mm-30) REVERT: F 24 GLN cc_start: 0.7535 (mt0) cc_final: 0.7106 (tm-30) REVERT: F 83 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7043 (mt-10) REVERT: A 80 LYS cc_start: 0.8448 (mtpt) cc_final: 0.7901 (ttmt) outliers start: 32 outliers final: 15 residues processed: 103 average time/residue: 0.2093 time to fit residues: 27.4849 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 : 1.648 ------------------------------------------------------------------------------- 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: 0.5980 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 = 0.4471 r_free = 0.4471 target = 0.155272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.133879 restraints weight = 7077.660| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.49 r_work: 0.4066 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3926 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4671 Z= 0.393 Angle : 0.789 5.404 6288 Z= 0.447 Chirality : 0.053 0.220 839 Planarity : 0.003 0.011 778 Dihedral : 9.302 44.419 687 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.41 % Favored : 80.59 % Rotamer: Outliers : 8.28 % Allowed : 13.51 % Favored : 78.21 % 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: -4.82 (0.29), residues: 639 helix: None (None), residues: 0 sheet: -3.56 (0.47), residues: 117 loop : -3.44 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 TYR 0.019 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 111 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 73 time to evaluate : 0.496 Fit side-chains REVERT: H 13 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6412 (mp0) REVERT: C 92 THR cc_start: 0.8090 (p) cc_final: 0.7712 (p) REVERT: I 13 GLU cc_start: 0.7616 (mt-10) cc_final: 0.6895 (tt0) REVERT: D 43 LYS cc_start: 0.8437 (tttt) cc_final: 0.7641 (mptt) REVERT: D 80 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8104 (mttp) REVERT: D 92 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.7995 (p) REVERT: J 12 LYS cc_start: 0.7452 (mttt) cc_final: 0.5682 (tmtt) REVERT: J 13 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7573 (tt0) REVERT: J 81 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7475 (p) REVERT: J 83 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7751 (mp0) REVERT: E 83 GLU cc_start: 0.8026 (mp0) cc_final: 0.7819 (mp0) REVERT: G 13 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6471 (mp0) REVERT: G 24 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7783 (tm-30) REVERT: B 80 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7971 (mtmt) REVERT: F 13 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6100 (tt0) REVERT: F 24 GLN cc_start: 0.7565 (mt0) cc_final: 0.7204 (tm-30) REVERT: F 83 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6925 (mt-10) REVERT: A 80 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8142 (mtpp) outliers start: 38 outliers final: 24 residues processed: 103 average time/residue: 0.1532 time to fit residues: 20.5399 Evaluate side-chains 95 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 0.0050 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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 = 0.4567 r_free = 0.4567 target = 0.160840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.138038 restraints weight = 6874.815| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.63 r_work: 0.4158 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4671 Z= 0.182 Angle : 0.668 5.624 6288 Z= 0.373 Chirality : 0.052 0.160 839 Planarity : 0.002 0.008 778 Dihedral : 8.010 38.257 687 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 6.54 % Allowed : 15.90 % Favored : 77.56 % 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: -4.26 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 TYR 0.010 0.002 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 107 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.490 Fit side-chains REVERT: H 13 GLU cc_start: 0.6482 (mt-10) cc_final: 0.5988 (tt0) REVERT: C 80 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7759 (mtmt) REVERT: C 83 GLU cc_start: 0.8022 (mp0) cc_final: 0.7793 (mp0) REVERT: C 92 THR cc_start: 0.7873 (p) cc_final: 0.7473 (p) REVERT: I 13 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6606 (tt0) REVERT: D 43 LYS cc_start: 0.8229 (tttt) cc_final: 0.7507 (mptt) REVERT: D 80 LYS cc_start: 0.8378 (mtpt) cc_final: 0.7927 (mttp) REVERT: D 83 GLU cc_start: 0.7994 (mp0) cc_final: 0.7767 (mp0) REVERT: D 92 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7697 (p) REVERT: J 12 LYS cc_start: 0.7189 (mttt) cc_final: 0.5584 (tmtt) REVERT: J 13 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7329 (tt0) REVERT: J 81 THR cc_start: 0.7448 (OUTLIER) cc_final: 0.7206 (p) REVERT: J 83 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7532 (mp0) REVERT: G 13 GLU cc_start: 0.6513 (mt-10) cc_final: 0.6181 (mp0) REVERT: B 80 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7677 (mttp) REVERT: B 83 GLU cc_start: 0.8055 (mp0) cc_final: 0.7757 (mp0) REVERT: F 24 GLN cc_start: 0.7514 (mt0) cc_final: 0.7162 (tm-30) REVERT: F 83 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7049 (mt-10) outliers start: 30 outliers final: 17 residues processed: 100 average time/residue: 0.1497 time to fit residues: 19.3011 Evaluate side-chains 89 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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 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: 0.0970 chunk 34 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 36 optimal weight: 0.0970 chunk 35 optimal weight: 0.1980 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 overall best weight: 0.2976 ------------------------------------------------------------------------------- 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 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 = 0.4658 r_free = 0.4658 target = 0.168015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.144724 restraints weight = 6776.629| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.63 r_work: 0.4225 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4671 Z= 0.145 Angle : 0.588 5.594 6288 Z= 0.327 Chirality : 0.050 0.132 839 Planarity : 0.001 0.009 778 Dihedral : 6.883 37.177 686 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.34 % Favored : 84.66 % Rotamer: Outliers : 6.10 % Allowed : 15.25 % Favored : 78.65 % 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: -4.01 (0.29), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 TYR 0.007 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 98 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.520 Fit side-chains REVERT: H 13 GLU cc_start: 0.6231 (mt-10) cc_final: 0.5593 (mp0) REVERT: H 62 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7157 (mp10) REVERT: H 83 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7452 (mp0) REVERT: C 43 LYS cc_start: 0.8155 (tttt) cc_final: 0.7404 (mptt) REVERT: C 80 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7695 (mtmt) REVERT: C 83 GLU cc_start: 0.8054 (mp0) cc_final: 0.7832 (mp0) REVERT: C 92 THR cc_start: 0.7811 (p) cc_final: 0.7414 (p) REVERT: I 13 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6570 (tt0) REVERT: D 43 LYS cc_start: 0.8127 (tttt) cc_final: 0.7446 (mptt) REVERT: D 80 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7880 (mttp) REVERT: D 83 GLU cc_start: 0.7983 (mp0) cc_final: 0.7731 (mp0) REVERT: D 92 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7622 (p) REVERT: J 13 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7275 (tt0) REVERT: J 83 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7650 (mp0) REVERT: E 83 GLU cc_start: 0.7848 (mp0) cc_final: 0.7599 (mp0) REVERT: G 13 GLU cc_start: 0.6256 (mt-10) cc_final: 0.6030 (mp0) REVERT: B 80 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7854 (mtmt) REVERT: F 24 GLN cc_start: 0.7461 (mt0) cc_final: 0.7117 (tm-30) REVERT: F 83 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7121 (mt-10) REVERT: A 83 GLU cc_start: 0.7820 (mp0) cc_final: 0.7552 (mp0) outliers start: 28 outliers final: 18 residues processed: 95 average time/residue: 0.1517 time to fit residues: 18.6846 Evaluate side-chains 87 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 62 GLN 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 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 88 ILE Chi-restraints excluded: chain B residue 62 GLN 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: 7.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.159329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.138532 restraints weight = 7047.406| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.31 r_work: 0.4122 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4671 Z= 0.378 Angle : 0.730 5.258 6288 Z= 0.412 Chirality : 0.053 0.140 839 Planarity : 0.003 0.009 778 Dihedral : 8.078 38.608 685 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.47 % Favored : 81.53 % Rotamer: Outliers : 8.06 % Allowed : 16.12 % Favored : 75.82 % 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: -4.11 (0.29), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 TYR 0.019 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 102 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 0.606 Fit side-chains REVERT: H 13 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6114 (mp0) REVERT: H 24 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7592 (tm-30) REVERT: H 46 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.6719 (tm-30) REVERT: C 83 GLU cc_start: 0.8160 (mp0) cc_final: 0.7681 (mp0) REVERT: C 92 THR cc_start: 0.8079 (p) cc_final: 0.7666 (p) REVERT: I 13 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6829 (tt0) REVERT: D 80 LYS cc_start: 0.8390 (mtpt) cc_final: 0.8088 (mttp) REVERT: D 92 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7959 (p) REVERT: J 12 LYS cc_start: 0.7424 (mttt) cc_final: 0.5856 (tmtt) REVERT: J 13 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7553 (tt0) REVERT: J 81 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7400 (p) REVERT: J 83 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7809 (mp0) REVERT: G 13 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6459 (mp0) REVERT: G 24 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7540 (tm-30) REVERT: G 46 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6658 (tm-30) REVERT: G 62 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: B 80 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7858 (mttp) REVERT: F 24 GLN cc_start: 0.7609 (mt0) cc_final: 0.7129 (tm-30) REVERT: F 83 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7011 (mt-10) REVERT: A 83 GLU cc_start: 0.7989 (mp0) cc_final: 0.7521 (mp0) outliers start: 37 outliers final: 25 residues processed: 96 average time/residue: 0.1445 time to fit residues: 18.4544 Evaluate side-chains 95 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 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 62 GLN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.158043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.136958 restraints weight = 6959.511| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.41 r_work: 0.4097 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4671 Z= 0.368 Angle : 0.745 5.154 6288 Z= 0.422 Chirality : 0.054 0.179 839 Planarity : 0.003 0.010 778 Dihedral : 8.260 39.053 685 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.09 % Favored : 80.91 % Rotamer: Outliers : 8.50 % Allowed : 16.12 % Favored : 75.38 % 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: -4.30 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 TYR 0.018 0.003 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 102 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 63 time to evaluate : 0.449 Fit side-chains REVERT: H 13 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6076 (mp0) REVERT: H 24 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7586 (tm-30) REVERT: H 46 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: C 80 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7825 (mtmt) REVERT: C 83 GLU cc_start: 0.8189 (mp0) cc_final: 0.7789 (mp0) REVERT: C 92 THR cc_start: 0.8139 (p) cc_final: 0.7751 (p) REVERT: I 13 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6772 (tt0) REVERT: D 80 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8138 (mttp) REVERT: D 83 GLU cc_start: 0.8137 (mp0) cc_final: 0.7921 (mp0) REVERT: D 92 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7978 (p) REVERT: J 12 LYS cc_start: 0.7477 (mttt) cc_final: 0.5933 (tmtt) REVERT: J 13 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7528 (tt0) REVERT: J 81 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7517 (p) REVERT: J 83 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7831 (mp0) REVERT: G 13 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6498 (mp0) REVERT: G 24 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7569 (tm-30) REVERT: G 46 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.6774 (tm-30) REVERT: B 80 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7931 (mttp) REVERT: F 24 GLN cc_start: 0.7628 (mt0) cc_final: 0.7135 (tm-30) REVERT: F 83 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7049 (mt-10) outliers start: 39 outliers final: 25 residues processed: 95 average time/residue: 0.1262 time to fit residues: 16.0945 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 : 0.537 ------------------------------------------------------------------------------- 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 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 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 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 62 GLN Chi-restraints excluded: chain A residue 63 VAL 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: 3.9990 chunk 20 optimal weight: 0.2980 chunk 11 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.0970 chunk 61 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.0978 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.160766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.138044 restraints weight = 6804.061| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.62 r_work: 0.4146 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4671 Z= 0.191 Angle : 0.643 5.544 6288 Z= 0.360 Chirality : 0.051 0.146 839 Planarity : 0.002 0.011 778 Dihedral : 7.421 39.106 685 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.81 % Favored : 84.19 % Rotamer: Outliers : 6.32 % Allowed : 17.43 % Favored : 76.25 % 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: -4.04 (0.29), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 TYR 0.010 0.002 TYR B 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 93 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.634 Fit side-chains REVERT: H 13 GLU cc_start: 0.6446 (mt-10) cc_final: 0.5928 (tt0) REVERT: H 83 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7637 (mp0) REVERT: C 80 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7707 (mtmt) REVERT: C 83 GLU cc_start: 0.8069 (mp0) cc_final: 0.7690 (mp0) REVERT: C 92 THR cc_start: 0.7942 (p) cc_final: 0.7534 (p) REVERT: I 13 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6458 (tt0) REVERT: D 80 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7928 (mttp) REVERT: D 83 GLU cc_start: 0.7947 (mp0) cc_final: 0.7731 (mp0) REVERT: D 92 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7680 (p) REVERT: J 12 LYS cc_start: 0.7254 (mttt) cc_final: 0.5660 (tmtt) REVERT: J 13 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7424 (tt0) REVERT: J 81 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.7082 (p) REVERT: J 83 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7692 (mp0) REVERT: G 13 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6186 (tt0) REVERT: G 46 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: B 80 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7846 (mttp) REVERT: F 24 GLN cc_start: 0.7567 (mt0) cc_final: 0.7088 (tm-30) REVERT: F 83 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7109 (mt-10) REVERT: A 83 GLU cc_start: 0.7920 (mp0) cc_final: 0.7621 (mp0) outliers start: 29 outliers final: 22 residues processed: 89 average time/residue: 0.1291 time to fit residues: 15.5517 Evaluate side-chains 90 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 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 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 62 GLN Chi-restraints excluded: chain F residue 88 ILE 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: 0.0670 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 0.0000 chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.6128 ------------------------------------------------------------------------------- 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 A 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.156108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.133497 restraints weight = 6967.741| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.63 r_work: 0.4089 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4671 Z= 0.331 Angle : 0.729 5.977 6288 Z= 0.409 Chirality : 0.053 0.152 839 Planarity : 0.002 0.010 778 Dihedral : 7.969 39.170 685 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.56 % Favored : 80.44 % Rotamer: Outliers : 7.63 % Allowed : 16.56 % Favored : 75.82 % 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 0.003 0.001 HIS E 50 TYR 0.017 0.003 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 99 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 0.457 Fit side-chains REVERT: H 13 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6000 (mp0) REVERT: H 46 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.6596 (tm-30) REVERT: H 83 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7715 (mp0) REVERT: C 80 LYS cc_start: 0.8337 (mtpt) cc_final: 0.7830 (mtmt) REVERT: C 92 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7593 (p) REVERT: I 13 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6725 (tt0) REVERT: I 46 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.6677 (tm-30) REVERT: D 80 LYS cc_start: 0.8376 (mtpt) cc_final: 0.8075 (mttp) REVERT: D 83 GLU cc_start: 0.8023 (mp0) cc_final: 0.7796 (mp0) REVERT: D 92 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7806 (p) REVERT: J 12 LYS cc_start: 0.7316 (mttt) cc_final: 0.5833 (tmtt) REVERT: J 13 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7546 (tt0) REVERT: J 81 THR cc_start: 0.7701 (OUTLIER) cc_final: 0.7287 (p) REVERT: J 83 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7721 (mp0) REVERT: G 13 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6483 (mp0) REVERT: G 24 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7796 (tm-30) REVERT: G 46 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: B 80 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7889 (mttp) REVERT: F 24 GLN cc_start: 0.7612 (mt0) cc_final: 0.7103 (tm-30) REVERT: F 83 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7031 (mt-10) REVERT: A 83 GLU cc_start: 0.7898 (mp0) cc_final: 0.7566 (mp0) outliers start: 35 outliers final: 24 residues processed: 91 average time/residue: 0.1366 time to fit residues: 16.4852 Evaluate side-chains 95 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 46 GLU 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 A 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.159735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.138281 restraints weight = 6994.352| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.42 r_work: 0.4116 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3974 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4671 Z= 0.325 Angle : 0.743 6.077 6288 Z= 0.417 Chirality : 0.053 0.149 839 Planarity : 0.002 0.010 778 Dihedral : 8.030 39.034 685 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.15 % Favored : 81.85 % Rotamer: Outliers : 7.41 % Allowed : 16.56 % Favored : 76.03 % 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: -4.20 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 TYR 0.016 0.003 TYR D 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 99 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 0.528 Fit side-chains REVERT: H 13 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6023 (mp0) REVERT: H 46 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: H 83 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7857 (mp0) REVERT: C 80 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7770 (mtmt) REVERT: C 83 GLU cc_start: 0.8153 (mp0) cc_final: 0.7943 (mp0) REVERT: C 92 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7763 (p) REVERT: I 13 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6689 (tt0) REVERT: D 80 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8013 (mttp) REVERT: D 83 GLU cc_start: 0.8152 (mp0) cc_final: 0.7846 (mp0) REVERT: D 92 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7911 (p) REVERT: J 12 LYS cc_start: 0.7433 (mttt) cc_final: 0.5972 (tmtt) REVERT: J 13 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7560 (tt0) REVERT: J 81 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7422 (p) REVERT: J 83 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7819 (mp0) REVERT: G 13 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6340 (tt0) REVERT: G 24 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7808 (tm-30) REVERT: G 46 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: B 80 LYS cc_start: 0.8389 (mtpt) cc_final: 0.7919 (mttp) REVERT: F 24 GLN cc_start: 0.7650 (mt0) cc_final: 0.7107 (tm-30) REVERT: F 83 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7108 (mt-10) REVERT: A 83 GLU cc_start: 0.7992 (mp0) cc_final: 0.7637 (mp0) outliers start: 34 outliers final: 25 residues processed: 91 average time/residue: 0.1411 time to fit residues: 17.0262 Evaluate side-chains 95 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 92 THR 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 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 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 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: 5.9990 chunk 52 optimal weight: 6.9990 chunk 37 optimal weight: 0.0770 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- 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 = 0.4523 r_free = 0.4523 target = 0.158635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.137435 restraints weight = 7061.861| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.41 r_work: 0.4127 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3993 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4671 Z= 0.374 Angle : 0.772 6.434 6288 Z= 0.437 Chirality : 0.054 0.151 839 Planarity : 0.003 0.011 778 Dihedral : 8.183 39.073 685 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.28 % Favored : 78.72 % Rotamer: Outliers : 7.41 % Allowed : 16.34 % Favored : 76.25 % 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: -4.33 (0.28), 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 0.003 0.001 HIS C 50 TYR 0.018 0.003 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.97 seconds wall clock time: 44 minutes 27.97 seconds (2667.97 seconds total)