Starting phenix.real_space_refine on Thu Sep 18 05:15:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyh_47304/09_2025/9dyh_47304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyh_47304/09_2025/9dyh_47304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dyh_47304/09_2025/9dyh_47304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyh_47304/09_2025/9dyh_47304.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dyh_47304/09_2025/9dyh_47304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyh_47304/09_2025/9dyh_47304.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 80 5.16 5 C 9415 2.51 5 N 2355 2.21 5 O 2485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14340 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2935 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: E, D, B, C Time building chain proxies: 3.32, per 1000 atoms: 0.23 Number of scatterers: 14340 At special positions: 0 Unit cell: (91.575, 92.4, 108.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 80 16.00 O 2485 8.00 N 2355 7.00 C 9415 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: 1.21 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.584A pdb=" N LEU A 22 " --> pdb=" O GLN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.654A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.503A pdb=" N VAL A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 296 removed outlier: 4.405A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.584A pdb=" N LEU E 22 " --> pdb=" O GLN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.654A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.504A pdb=" N VAL E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 296 removed outlier: 4.405A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 323 Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 17 through 23 removed outlier: 3.584A pdb=" N LEU D 22 " --> pdb=" O GLN D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.653A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 77 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.503A pdb=" N VAL D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 296 removed outlier: 4.405A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 323 Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.584A pdb=" N LEU B 22 " --> pdb=" O GLN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.654A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.503A pdb=" N VAL B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 296 removed outlier: 4.405A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 323 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.584A pdb=" N LEU C 22 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.654A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.503A pdb=" N VAL C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 296 removed outlier: 4.406A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 323 975 hydrogen bonds defined for protein. 2815 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: 2.49 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2549 1.32 - 1.45: 4164 1.45 - 1.57: 7892 1.57 - 1.70: 0 1.70 - 1.83: 120 Bond restraints: 14725 Sorted by residual: bond pdb=" CA VAL C 183 " pdb=" CB VAL C 183 " ideal model delta sigma weight residual 1.539 1.518 0.021 5.40e-03 3.43e+04 1.58e+01 bond pdb=" CA VAL D 183 " pdb=" CB VAL D 183 " ideal model delta sigma weight residual 1.539 1.518 0.021 5.40e-03 3.43e+04 1.58e+01 bond pdb=" CA VAL A 183 " pdb=" CB VAL A 183 " ideal model delta sigma weight residual 1.539 1.518 0.021 5.40e-03 3.43e+04 1.56e+01 bond pdb=" CA VAL B 183 " pdb=" CB VAL B 183 " ideal model delta sigma weight residual 1.539 1.518 0.021 5.40e-03 3.43e+04 1.47e+01 bond pdb=" CA VAL E 183 " pdb=" CB VAL E 183 " ideal model delta sigma weight residual 1.539 1.518 0.021 5.40e-03 3.43e+04 1.47e+01 ... (remaining 14720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 12659 1.27 - 2.54: 6101 2.54 - 3.81: 1126 3.81 - 5.07: 77 5.07 - 6.34: 17 Bond angle restraints: 19980 Sorted by residual: angle pdb=" N THR D 277 " pdb=" CA THR D 277 " pdb=" C THR D 277 " ideal model delta sigma weight residual 111.28 104.94 6.34 1.09e+00 8.42e-01 3.39e+01 angle pdb=" N THR B 277 " pdb=" CA THR B 277 " pdb=" C THR B 277 " ideal model delta sigma weight residual 111.28 104.95 6.33 1.09e+00 8.42e-01 3.37e+01 angle pdb=" N THR A 277 " pdb=" CA THR A 277 " pdb=" C THR A 277 " ideal model delta sigma weight residual 111.28 104.97 6.31 1.09e+00 8.42e-01 3.35e+01 angle pdb=" N THR C 277 " pdb=" CA THR C 277 " pdb=" C THR C 277 " ideal model delta sigma weight residual 111.28 104.98 6.30 1.09e+00 8.42e-01 3.34e+01 angle pdb=" N THR E 277 " pdb=" CA THR E 277 " pdb=" C THR E 277 " ideal model delta sigma weight residual 111.28 105.02 6.26 1.09e+00 8.42e-01 3.30e+01 ... (remaining 19975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 7480 16.16 - 32.33: 720 32.33 - 48.49: 240 48.49 - 64.66: 55 64.66 - 80.82: 20 Dihedral angle restraints: 8515 sinusoidal: 3385 harmonic: 5130 Sorted by residual: dihedral pdb=" CA LEU E 329 " pdb=" C LEU E 329 " pdb=" N ALA E 330 " pdb=" CA ALA E 330 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA LEU C 329 " pdb=" C LEU C 329 " pdb=" N ALA C 330 " pdb=" CA ALA C 330 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA LEU A 329 " pdb=" C LEU A 329 " pdb=" N ALA A 330 " pdb=" CA ALA A 330 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 8512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 886 0.039 - 0.078: 616 0.078 - 0.117: 460 0.117 - 0.156: 157 0.156 - 0.195: 51 Chirality restraints: 2170 Sorted by residual: chirality pdb=" CB ILE E 28 " pdb=" CA ILE E 28 " pdb=" CG1 ILE E 28 " pdb=" CG2 ILE E 28 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA VAL E 3 " pdb=" N VAL E 3 " pdb=" C VAL E 3 " pdb=" CB VAL E 3 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CB ILE A 28 " pdb=" CA ILE A 28 " pdb=" CG1 ILE A 28 " pdb=" CG2 ILE A 28 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 2167 not shown) Planarity restraints: 2495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 182 " -0.038 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP A 182 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 182 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 182 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 182 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP A 182 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 182 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 182 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 182 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 182 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 182 " 0.038 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP B 182 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 182 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 182 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP B 182 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP B 182 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 182 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 182 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 182 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 182 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 182 " -0.038 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP D 182 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP D 182 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP D 182 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP D 182 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP D 182 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 182 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 182 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 182 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 182 " -0.028 2.00e-02 2.50e+03 ... (remaining 2492 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 113 2.57 - 3.16: 11945 3.16 - 3.74: 24722 3.74 - 4.32: 35265 4.32 - 4.90: 55616 Nonbonded interactions: 127661 Sorted by model distance: nonbonded pdb=" OG1 THR E 237 " pdb=" OH TYR D 5 " model vdw 1.993 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" OG1 THR B 237 " model vdw 2.004 3.040 nonbonded pdb=" OG1 THR A 237 " pdb=" OH TYR E 5 " model vdw 2.011 3.040 nonbonded pdb=" OH TYR B 5 " pdb=" OG1 THR C 237 " model vdw 2.012 3.040 nonbonded pdb=" OG1 THR D 237 " pdb=" OH TYR C 5 " model vdw 2.018 3.040 ... (remaining 127656 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'D' selection = chain 'B' selection = chain 'C' } 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=0.50 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: 6.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.210 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.012 0.058 14725 Z= 0.896 Angle : 1.367 6.343 19980 Z= 1.053 Chirality : 0.072 0.195 2170 Planarity : 0.006 0.023 2495 Dihedral : 15.273 80.825 5225 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.64 % Allowed : 9.87 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.19), residues: 1710 helix: 1.32 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : -0.28 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 313 TYR 0.045 0.009 TYR D 124 PHE 0.035 0.007 PHE E 171 TRP 0.038 0.010 TRP A 182 HIS 0.005 0.002 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.01227 (14725) covalent geometry : angle 1.36702 (19980) hydrogen bonds : bond 0.13785 ( 975) hydrogen bonds : angle 5.13391 ( 2815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 457 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8453 (tp) cc_final: 0.8188 (tt) REVERT: A 34 ARG cc_start: 0.6764 (mtt90) cc_final: 0.6081 (mtm180) REVERT: A 58 GLN cc_start: 0.6960 (mt0) cc_final: 0.6635 (mt0) REVERT: A 63 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7119 (mt-10) REVERT: A 71 GLN cc_start: 0.7154 (tt0) cc_final: 0.6172 (mm110) REVERT: A 91 ASN cc_start: 0.8531 (m-40) cc_final: 0.8170 (m110) REVERT: A 197 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.8086 (ttm-80) REVERT: A 249 LEU cc_start: 0.7236 (mt) cc_final: 0.7030 (mp) REVERT: E 29 TYR cc_start: 0.8312 (m-80) cc_final: 0.8062 (m-80) REVERT: E 34 ARG cc_start: 0.6879 (mtt90) cc_final: 0.6231 (mtm180) REVERT: E 71 GLN cc_start: 0.7409 (tt0) cc_final: 0.7166 (tt0) REVERT: E 170 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6314 (mtmt) REVERT: E 197 ARG cc_start: 0.8473 (ttp-110) cc_final: 0.8032 (ttm-80) REVERT: E 202 ARG cc_start: 0.7793 (mtt180) cc_final: 0.7420 (mtp-110) REVERT: D 32 LEU cc_start: 0.8053 (tp) cc_final: 0.7630 (tt) REVERT: D 34 ARG cc_start: 0.7053 (mtt90) cc_final: 0.6256 (mtm180) REVERT: D 63 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7125 (mp0) REVERT: D 91 ASN cc_start: 0.8752 (m-40) cc_final: 0.8439 (m110) REVERT: D 149 LYS cc_start: 0.8256 (mttp) cc_final: 0.8009 (mttt) REVERT: D 166 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8129 (mm-30) REVERT: D 170 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6626 (mtpt) REVERT: D 197 ARG cc_start: 0.8413 (ttp-110) cc_final: 0.8059 (ttm-80) REVERT: D 202 ARG cc_start: 0.8121 (mtt180) cc_final: 0.7333 (mtp-110) REVERT: D 249 LEU cc_start: 0.7409 (mt) cc_final: 0.7119 (mp) REVERT: D 306 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7326 (mm-30) REVERT: D 316 GLN cc_start: 0.8088 (tm130) cc_final: 0.7608 (tt0) REVERT: D 336 LEU cc_start: 0.6930 (tp) cc_final: 0.6695 (tp) REVERT: B 14 PHE cc_start: 0.7598 (t80) cc_final: 0.7066 (t80) REVERT: B 32 LEU cc_start: 0.8321 (tp) cc_final: 0.7941 (tt) REVERT: B 38 CYS cc_start: 0.8077 (m) cc_final: 0.7597 (t) REVERT: B 170 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6742 (mtmt) REVERT: B 213 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6826 (mm-30) REVERT: B 276 PHE cc_start: 0.6674 (m-80) cc_final: 0.6404 (m-80) REVERT: B 282 PHE cc_start: 0.7726 (t80) cc_final: 0.7171 (t80) REVERT: B 325 MET cc_start: 0.8073 (mtp) cc_final: 0.7731 (mtp) REVERT: C 34 ARG cc_start: 0.7153 (mtt90) cc_final: 0.6527 (mtm180) REVERT: C 202 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7234 (mtp-110) REVERT: C 282 PHE cc_start: 0.7640 (t80) cc_final: 0.7374 (t80) outliers start: 25 outliers final: 0 residues processed: 468 average time/residue: 0.1481 time to fit residues: 97.6008 Evaluate side-chains 240 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 237 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain B residue 170 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 173 ASN A 316 GLN A 361 GLN E 316 GLN E 361 GLN D 156 HIS D 173 ASN D 361 GLN B 91 ASN B 238 GLN B 267 HIS B 361 GLN C 96 GLN C 156 HIS C 204 ASN C 361 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150167 restraints weight = 38504.395| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.16 r_work: 0.3575 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14725 Z= 0.155 Angle : 0.603 10.907 19980 Z= 0.322 Chirality : 0.041 0.188 2170 Planarity : 0.004 0.048 2495 Dihedral : 4.646 41.218 1972 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.97 % Allowed : 12.37 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.20), residues: 1710 helix: 1.35 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.21 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 218 TYR 0.029 0.002 TYR D 43 PHE 0.039 0.002 PHE E 42 TRP 0.015 0.002 TRP B 94 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00320 (14725) covalent geometry : angle 0.60331 (19980) hydrogen bonds : bond 0.05876 ( 975) hydrogen bonds : angle 4.78099 ( 2815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8355 (mtp85) cc_final: 0.7906 (mtp85) REVERT: A 19 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7043 (pp30) REVERT: A 34 ARG cc_start: 0.7268 (mtt90) cc_final: 0.6866 (mtm180) REVERT: A 71 GLN cc_start: 0.6844 (tt0) cc_final: 0.5902 (mm110) REVERT: A 91 ASN cc_start: 0.8952 (m-40) cc_final: 0.8474 (m110) REVERT: E 19 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6568 (mm110) REVERT: E 34 ARG cc_start: 0.7327 (mtt90) cc_final: 0.6740 (mtm180) REVERT: E 44 MET cc_start: 0.7261 (mmm) cc_final: 0.7017 (mmm) REVERT: E 202 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7261 (mtp-110) REVERT: E 306 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6886 (mp0) REVERT: D 19 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6142 (mm110) REVERT: D 32 LEU cc_start: 0.8288 (tp) cc_final: 0.8026 (tt) REVERT: D 91 ASN cc_start: 0.8885 (m-40) cc_final: 0.8519 (m110) REVERT: D 149 LYS cc_start: 0.8389 (mttp) cc_final: 0.8113 (mttt) REVERT: D 202 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7254 (mtp-110) REVERT: D 245 TYR cc_start: 0.7461 (m-10) cc_final: 0.7193 (m-80) REVERT: D 306 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 23 LEU cc_start: 0.7309 (mp) cc_final: 0.7054 (mp) REVERT: B 32 LEU cc_start: 0.8445 (tp) cc_final: 0.8106 (tt) REVERT: B 36 LEU cc_start: 0.8689 (tp) cc_final: 0.8420 (mp) REVERT: B 173 ASN cc_start: 0.8103 (m-40) cc_final: 0.7815 (m-40) REVERT: B 249 LEU cc_start: 0.7633 (mt) cc_final: 0.7373 (mp) REVERT: B 282 PHE cc_start: 0.8093 (t80) cc_final: 0.7860 (t80) REVERT: C 34 ARG cc_start: 0.7634 (mtt90) cc_final: 0.7266 (mtm180) REVERT: C 168 ARG cc_start: 0.7221 (tmt90) cc_final: 0.6816 (tmm-80) REVERT: C 202 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7118 (mtp-110) REVERT: C 282 PHE cc_start: 0.7891 (t80) cc_final: 0.7594 (t80) outliers start: 30 outliers final: 12 residues processed: 292 average time/residue: 0.1334 time to fit residues: 56.8400 Evaluate side-chains 239 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 177 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 267 HIS E 156 HIS E 204 ASN D 173 ASN B 91 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.168035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.149223 restraints weight = 39997.802| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.02 r_work: 0.3548 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14725 Z= 0.163 Angle : 0.586 8.953 19980 Z= 0.313 Chirality : 0.042 0.200 2170 Planarity : 0.004 0.053 2495 Dihedral : 4.088 18.552 1960 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.45 % Allowed : 13.88 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.20), residues: 1710 helix: 1.25 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.17 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 218 TYR 0.025 0.002 TYR A 43 PHE 0.051 0.002 PHE E 42 TRP 0.013 0.002 TRP B 33 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00351 (14725) covalent geometry : angle 0.58636 (19980) hydrogen bonds : bond 0.05473 ( 975) hydrogen bonds : angle 4.74496 ( 2815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 CYS cc_start: 0.7845 (p) cc_final: 0.7622 (p) REVERT: A 44 MET cc_start: 0.7608 (mmm) cc_final: 0.7408 (mmm) REVERT: E 19 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6281 (mm110) REVERT: E 34 ARG cc_start: 0.7498 (mtt90) cc_final: 0.6994 (mtm180) REVERT: E 44 MET cc_start: 0.7308 (mmm) cc_final: 0.6698 (mmm) REVERT: E 47 SER cc_start: 0.6772 (t) cc_final: 0.6441 (p) REVERT: D 19 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6176 (mm110) REVERT: D 149 LYS cc_start: 0.8499 (mttp) cc_final: 0.8232 (mttt) REVERT: D 173 ASN cc_start: 0.7925 (m-40) cc_final: 0.7708 (m-40) REVERT: D 202 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7458 (mtp-110) REVERT: D 218 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7515 (ttp80) REVERT: B 173 ASN cc_start: 0.8234 (m-40) cc_final: 0.7981 (m-40) REVERT: B 249 LEU cc_start: 0.7762 (mt) cc_final: 0.7517 (mp) REVERT: B 282 PHE cc_start: 0.8129 (t80) cc_final: 0.7868 (t80) REVERT: C 34 ARG cc_start: 0.7829 (mtt90) cc_final: 0.7555 (mtm180) REVERT: C 202 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7315 (mtp-110) outliers start: 22 outliers final: 15 residues processed: 273 average time/residue: 0.1354 time to fit residues: 53.8017 Evaluate side-chains 242 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 169 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 173 ASN E 204 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 204 ASN B 96 GLN B 115 HIS B 204 ASN C 91 ASN C 173 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.165257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148302 restraints weight = 28822.604| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.42 r_work: 0.3580 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14725 Z= 0.158 Angle : 0.579 10.649 19980 Z= 0.309 Chirality : 0.042 0.197 2170 Planarity : 0.004 0.053 2495 Dihedral : 4.025 19.992 1960 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.71 % Allowed : 14.08 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.20), residues: 1710 helix: 1.25 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.17 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 218 TYR 0.024 0.002 TYR A 43 PHE 0.051 0.002 PHE E 42 TRP 0.012 0.001 TRP E 94 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00343 (14725) covalent geometry : angle 0.57936 (19980) hydrogen bonds : bond 0.05313 ( 975) hydrogen bonds : angle 4.72723 ( 2815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 CYS cc_start: 0.7766 (p) cc_final: 0.7545 (p) REVERT: E 19 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6073 (mm110) REVERT: E 44 MET cc_start: 0.7295 (mmm) cc_final: 0.6602 (mmm) REVERT: E 47 SER cc_start: 0.6956 (t) cc_final: 0.6459 (p) REVERT: E 301 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: D 19 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6140 (mm110) REVERT: D 149 LYS cc_start: 0.8462 (mttp) cc_final: 0.8243 (mttt) REVERT: D 202 ARG cc_start: 0.7882 (mtt180) cc_final: 0.7538 (mtp-110) REVERT: D 218 ARG cc_start: 0.7856 (ttp80) cc_final: 0.7501 (ttp80) REVERT: B 71 GLN cc_start: 0.7225 (tt0) cc_final: 0.6993 (tt0) REVERT: B 173 ASN cc_start: 0.8218 (m-40) cc_final: 0.7921 (m-40) REVERT: B 218 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7163 (ttp80) REVERT: B 282 PHE cc_start: 0.8108 (t80) cc_final: 0.7886 (t80) REVERT: C 34 ARG cc_start: 0.7755 (mtt90) cc_final: 0.7472 (mtm180) REVERT: C 202 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7413 (mtp-110) outliers start: 26 outliers final: 16 residues processed: 268 average time/residue: 0.1236 time to fit residues: 49.3049 Evaluate side-chains 238 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 157 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS D 173 ASN D 204 ASN C 204 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.164602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147087 restraints weight = 32066.105| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.60 r_work: 0.3556 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14725 Z= 0.160 Angle : 0.583 12.955 19980 Z= 0.310 Chirality : 0.042 0.201 2170 Planarity : 0.004 0.041 2495 Dihedral : 4.032 20.855 1960 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.11 % Allowed : 14.41 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.20), residues: 1710 helix: 1.33 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.30 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 218 TYR 0.024 0.002 TYR A 43 PHE 0.052 0.002 PHE E 42 TRP 0.014 0.001 TRP A 93 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00352 (14725) covalent geometry : angle 0.58321 (19980) hydrogen bonds : bond 0.05255 ( 975) hydrogen bonds : angle 4.71615 ( 2815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 CYS cc_start: 0.7684 (p) cc_final: 0.7019 (p) REVERT: A 203 ASP cc_start: 0.7654 (p0) cc_final: 0.6949 (m-30) REVERT: E 19 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6866 (pp30) REVERT: E 44 MET cc_start: 0.7249 (mmm) cc_final: 0.6944 (mmm) REVERT: E 204 ASN cc_start: 0.7576 (m-40) cc_final: 0.7375 (m110) REVERT: E 301 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7240 (m-30) REVERT: D 19 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6150 (mm110) REVERT: D 149 LYS cc_start: 0.8449 (mttp) cc_final: 0.8233 (mttt) REVERT: D 202 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7599 (mtp-110) REVERT: D 218 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7472 (ttp80) REVERT: D 273 VAL cc_start: 0.6364 (t) cc_final: 0.6122 (p) REVERT: B 36 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8827 (mp) REVERT: B 71 GLN cc_start: 0.7281 (tt0) cc_final: 0.7043 (tt0) REVERT: B 173 ASN cc_start: 0.8230 (m-40) cc_final: 0.7916 (m-40) REVERT: B 282 PHE cc_start: 0.8062 (t80) cc_final: 0.7860 (t80) REVERT: C 34 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7464 (mtm180) REVERT: C 197 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8049 (ttp80) REVERT: C 202 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7380 (mtp-110) outliers start: 32 outliers final: 19 residues processed: 271 average time/residue: 0.1162 time to fit residues: 46.9759 Evaluate side-chains 249 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.163728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145367 restraints weight = 37128.747| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.86 r_work: 0.3533 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14725 Z= 0.161 Angle : 0.590 13.733 19980 Z= 0.312 Chirality : 0.042 0.203 2170 Planarity : 0.004 0.039 2495 Dihedral : 4.019 19.690 1960 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.04 % Allowed : 14.47 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.20), residues: 1710 helix: 1.31 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.34 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 218 TYR 0.023 0.002 TYR A 43 PHE 0.053 0.002 PHE B 42 TRP 0.012 0.001 TRP D 93 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00354 (14725) covalent geometry : angle 0.58955 (19980) hydrogen bonds : bond 0.05199 ( 975) hydrogen bonds : angle 4.73447 ( 2815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7890 (mtp180) REVERT: A 202 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7618 (mtp180) REVERT: A 203 ASP cc_start: 0.7589 (p0) cc_final: 0.7026 (m-30) REVERT: E 19 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6080 (mm110) REVERT: E 44 MET cc_start: 0.7284 (mmm) cc_final: 0.6975 (mmm) REVERT: E 63 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: E 301 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: D 19 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6552 (mm110) REVERT: D 149 LYS cc_start: 0.8482 (mttp) cc_final: 0.8177 (mttt) REVERT: D 202 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7625 (mtp-110) REVERT: B 71 GLN cc_start: 0.7339 (tt0) cc_final: 0.7105 (tt0) REVERT: B 173 ASN cc_start: 0.8218 (m-40) cc_final: 0.7884 (m-40) REVERT: C 34 ARG cc_start: 0.7748 (mtt90) cc_final: 0.7437 (mtm180) REVERT: C 44 MET cc_start: 0.7188 (mmm) cc_final: 0.6707 (mmp) REVERT: C 197 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8087 (ttp80) REVERT: C 202 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7472 (mtp-110) outliers start: 31 outliers final: 20 residues processed: 258 average time/residue: 0.1169 time to fit residues: 44.7604 Evaluate side-chains 241 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 319 MET Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 139 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 78 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN E 115 HIS E 204 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN B 190 ASN C 204 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.164685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147573 restraints weight = 29948.683| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.48 r_work: 0.3570 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14725 Z= 0.150 Angle : 0.587 13.975 19980 Z= 0.310 Chirality : 0.041 0.214 2170 Planarity : 0.004 0.033 2495 Dihedral : 3.993 20.200 1960 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.97 % Allowed : 14.87 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.20), residues: 1710 helix: 1.31 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.27 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 218 TYR 0.023 0.002 TYR A 43 PHE 0.052 0.002 PHE B 42 TRP 0.012 0.001 TRP E 94 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00325 (14725) covalent geometry : angle 0.58669 (19980) hydrogen bonds : bond 0.05082 ( 975) hydrogen bonds : angle 4.74973 ( 2815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 CYS cc_start: 0.7877 (p) cc_final: 0.7617 (p) REVERT: A 202 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7662 (mtp180) REVERT: A 203 ASP cc_start: 0.7604 (p0) cc_final: 0.7095 (m-30) REVERT: A 249 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7386 (mp) REVERT: E 19 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6556 (pp30) REVERT: E 44 MET cc_start: 0.7312 (mmm) cc_final: 0.7004 (mmm) REVERT: E 63 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: E 301 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: D 19 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6370 (mm110) REVERT: D 149 LYS cc_start: 0.8461 (mttp) cc_final: 0.8207 (mttt) REVERT: D 202 ARG cc_start: 0.7861 (mtt180) cc_final: 0.7633 (mtp-110) REVERT: D 273 VAL cc_start: 0.6449 (t) cc_final: 0.6243 (p) REVERT: D 316 GLN cc_start: 0.8253 (tt0) cc_final: 0.8017 (tt0) REVERT: B 71 GLN cc_start: 0.7414 (tt0) cc_final: 0.7177 (tt0) REVERT: B 173 ASN cc_start: 0.8193 (m-40) cc_final: 0.7849 (m-40) REVERT: C 34 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7402 (mtm180) REVERT: C 44 MET cc_start: 0.7196 (mmm) cc_final: 0.6702 (mmp) REVERT: C 202 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7602 (mtp-110) REVERT: C 316 GLN cc_start: 0.8276 (tp40) cc_final: 0.7857 (tt0) outliers start: 30 outliers final: 20 residues processed: 258 average time/residue: 0.1195 time to fit residues: 46.1479 Evaluate side-chains 246 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 115 optimal weight: 0.5980 chunk 163 optimal weight: 0.3980 chunk 160 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 100 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN C 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.164721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145148 restraints weight = 39530.900| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.22 r_work: 0.3545 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14725 Z= 0.141 Angle : 0.581 13.997 19980 Z= 0.305 Chirality : 0.041 0.215 2170 Planarity : 0.004 0.032 2495 Dihedral : 3.950 20.039 1960 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.91 % Allowed : 15.07 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.20), residues: 1710 helix: 1.39 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.24 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 218 TYR 0.022 0.002 TYR A 43 PHE 0.050 0.002 PHE B 42 TRP 0.012 0.001 TRP E 94 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00298 (14725) covalent geometry : angle 0.58074 (19980) hydrogen bonds : bond 0.04973 ( 975) hydrogen bonds : angle 4.71062 ( 2815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7760 (mtp180) REVERT: A 38 CYS cc_start: 0.8115 (p) cc_final: 0.7893 (p) REVERT: A 203 ASP cc_start: 0.7639 (p0) cc_final: 0.6926 (m-30) REVERT: A 249 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7177 (mp) REVERT: E 19 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6226 (pp30) REVERT: E 44 MET cc_start: 0.7093 (mmm) cc_final: 0.6771 (mmm) REVERT: E 63 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: D 19 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6479 (mm110) REVERT: D 149 LYS cc_start: 0.8177 (mttp) cc_final: 0.7936 (mttt) REVERT: D 202 ARG cc_start: 0.7818 (mtt180) cc_final: 0.7572 (mtp-110) REVERT: D 273 VAL cc_start: 0.6441 (t) cc_final: 0.6123 (p) REVERT: D 316 GLN cc_start: 0.8204 (tt0) cc_final: 0.7899 (tt0) REVERT: B 42 PHE cc_start: 0.7293 (m-80) cc_final: 0.6927 (m-80) REVERT: B 71 GLN cc_start: 0.7301 (tt0) cc_final: 0.7037 (tt0) REVERT: B 173 ASN cc_start: 0.8113 (m-40) cc_final: 0.7738 (m-40) REVERT: C 34 ARG cc_start: 0.7505 (mtt90) cc_final: 0.7084 (mtm180) REVERT: C 44 MET cc_start: 0.7066 (mmm) cc_final: 0.6572 (mmp) REVERT: C 316 GLN cc_start: 0.8283 (tp40) cc_final: 0.7706 (tt0) outliers start: 29 outliers final: 19 residues processed: 263 average time/residue: 0.1254 time to fit residues: 48.9364 Evaluate side-chains 246 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 319 MET Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 159 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.143834 restraints weight = 39964.846| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.25 r_work: 0.3526 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14725 Z= 0.156 Angle : 0.606 13.921 19980 Z= 0.316 Chirality : 0.042 0.211 2170 Planarity : 0.004 0.029 2495 Dihedral : 3.973 20.297 1960 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.64 % Allowed : 15.86 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.20), residues: 1710 helix: 1.28 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : -0.11 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 218 TYR 0.026 0.002 TYR B 85 PHE 0.049 0.002 PHE B 42 TRP 0.012 0.001 TRP D 93 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00344 (14725) covalent geometry : angle 0.60594 (19980) hydrogen bonds : bond 0.05031 ( 975) hydrogen bonds : angle 4.73155 ( 2815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 CYS cc_start: 0.8110 (p) cc_final: 0.7876 (p) REVERT: A 203 ASP cc_start: 0.7630 (p0) cc_final: 0.6941 (m-30) REVERT: A 249 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7129 (mp) REVERT: E 8 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7636 (mtp-110) REVERT: E 19 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6242 (pp30) REVERT: E 44 MET cc_start: 0.7066 (mmm) cc_final: 0.6739 (mmm) REVERT: E 63 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: E 301 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: D 19 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6421 (mm110) REVERT: D 149 LYS cc_start: 0.8190 (mttp) cc_final: 0.7903 (mttt) REVERT: D 202 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7388 (mtp-110) REVERT: D 273 VAL cc_start: 0.6470 (t) cc_final: 0.6165 (p) REVERT: D 316 GLN cc_start: 0.8231 (tt0) cc_final: 0.7922 (tt0) REVERT: B 71 GLN cc_start: 0.7364 (tt0) cc_final: 0.7109 (tt0) REVERT: B 117 ARG cc_start: 0.7366 (mtt-85) cc_final: 0.6913 (mmt180) REVERT: B 173 ASN cc_start: 0.8174 (m-40) cc_final: 0.7791 (m-40) REVERT: C 34 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7073 (mtm180) REVERT: C 44 MET cc_start: 0.7091 (mmm) cc_final: 0.6607 (mmp) REVERT: C 316 GLN cc_start: 0.8322 (tp40) cc_final: 0.7744 (tt0) outliers start: 25 outliers final: 16 residues processed: 252 average time/residue: 0.1128 time to fit residues: 42.5713 Evaluate side-chains 244 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 319 MET Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 159 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 168 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.162943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144252 restraints weight = 34809.013| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.98 r_work: 0.3540 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14725 Z= 0.158 Angle : 0.613 13.912 19980 Z= 0.319 Chirality : 0.042 0.211 2170 Planarity : 0.004 0.029 2495 Dihedral : 3.992 20.340 1960 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.51 % Allowed : 16.05 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.20), residues: 1710 helix: 1.34 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.32 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 218 TYR 0.030 0.002 TYR B 85 PHE 0.051 0.002 PHE B 42 TRP 0.012 0.001 TRP D 93 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00349 (14725) covalent geometry : angle 0.61296 (19980) hydrogen bonds : bond 0.05077 ( 975) hydrogen bonds : angle 4.74627 ( 2815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 CYS cc_start: 0.8155 (p) cc_final: 0.7937 (p) REVERT: A 203 ASP cc_start: 0.7592 (p0) cc_final: 0.6965 (m-30) REVERT: A 249 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7136 (mp) REVERT: E 8 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7615 (mtp-110) REVERT: E 19 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6161 (pp30) REVERT: E 44 MET cc_start: 0.7058 (mmm) cc_final: 0.6728 (mmm) REVERT: E 63 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: E 301 ASP cc_start: 0.7855 (m-30) cc_final: 0.7454 (m-30) REVERT: D 19 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6372 (mm110) REVERT: D 63 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: D 149 LYS cc_start: 0.8190 (mttp) cc_final: 0.7917 (mttt) REVERT: D 202 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7424 (mtp-110) REVERT: D 273 VAL cc_start: 0.6574 (t) cc_final: 0.6287 (p) REVERT: D 316 GLN cc_start: 0.8216 (tt0) cc_final: 0.7880 (tt0) REVERT: D 339 ASP cc_start: 0.6319 (m-30) cc_final: 0.6102 (m-30) REVERT: B 71 GLN cc_start: 0.7359 (tt0) cc_final: 0.7104 (tt0) REVERT: B 173 ASN cc_start: 0.8155 (m-40) cc_final: 0.7762 (m-40) REVERT: C 34 ARG cc_start: 0.7475 (mtt90) cc_final: 0.7078 (mtm180) REVERT: C 44 MET cc_start: 0.7067 (mmm) cc_final: 0.6588 (mmp) outliers start: 23 outliers final: 17 residues processed: 251 average time/residue: 0.1281 time to fit residues: 47.7319 Evaluate side-chains 248 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 319 MET Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 118 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 128 optimal weight: 0.0050 chunk 37 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.165420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145786 restraints weight = 37649.877| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.31 r_work: 0.3562 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14725 Z= 0.140 Angle : 0.602 14.096 19980 Z= 0.312 Chirality : 0.042 0.226 2170 Planarity : 0.004 0.032 2495 Dihedral : 3.956 19.784 1960 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.38 % Allowed : 16.38 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.20), residues: 1710 helix: 1.39 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.35 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 117 TYR 0.026 0.002 TYR B 85 PHE 0.050 0.002 PHE B 42 TRP 0.012 0.001 TRP D 93 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00298 (14725) covalent geometry : angle 0.60152 (19980) hydrogen bonds : bond 0.04922 ( 975) hydrogen bonds : angle 4.70038 ( 2815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.31 seconds wall clock time: 59 minutes 36.72 seconds (3576.72 seconds total)