Starting phenix.real_space_refine on Thu Jun 12 20:40:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyh_47304/06_2025/9dyh_47304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyh_47304/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dyh_47304/06_2025/9dyh_47304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyh_47304/06_2025/9dyh_47304.map" model { file = "/net/cci-nas-00/data/ceres_data/9dyh_47304/06_2025/9dyh_47304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyh_47304/06_2025/9dyh_47304.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D Time building chain proxies: 8.16, per 1000 atoms: 0.57 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: 3.42 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 1.19 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: 3.87 Time building geometry restraints manager: 4.07 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 4.300 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.340 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.450 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.038 0.010 TRP A 182 HIS 0.005 0.002 HIS A 115 PHE 0.035 0.007 PHE E 171 TYR 0.045 0.009 TYR D 124 ARG 0.013 0.002 ARG C 313 Details of bonding type rmsd hydrogen bonds : bond 0.13785 ( 975) hydrogen bonds : angle 5.13391 ( 2815) covalent geometry : bond 0.01227 (14725) covalent geometry : angle 1.36702 (19980) *********************** 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 : 1.700 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: 0.8171 (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: 0.8061 (m-80) REVERT: E 34 ARG cc_start: 0.6879 (mtt90) cc_final: 0.6230 (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: 0.7334 (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: 0.7598 (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: 0.7373 (t80) outliers start: 25 outliers final: 0 residues processed: 468 average time/residue: 0.3002 time to fit residues: 196.7576 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 : 1.705 ------------------------------------------------------------------------------- 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 143 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN A 316 GLN A 361 GLN E 316 GLN E 361 GLN ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 361 GLN B 91 ASN B 238 GLN B 361 GLN C 96 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN C 361 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.168504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.149655 restraints weight = 37864.355| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.00 r_work: 0.3580 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 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 = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14725 Z= 0.164 Angle : 0.614 11.275 19980 Z= 0.325 Chirality : 0.042 0.183 2170 Planarity : 0.004 0.048 2495 Dihedral : 4.628 40.436 1972 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.84 % Allowed : 12.43 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1710 helix: 1.28 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.13 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 94 HIS 0.002 0.001 HIS A 267 PHE 0.039 0.002 PHE E 42 TYR 0.030 0.002 TYR D 43 ARG 0.012 0.001 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.05792 ( 975) hydrogen bonds : angle 4.77468 ( 2815) covalent geometry : bond 0.00346 (14725) covalent geometry : angle 0.61429 (19980) *********************** 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 293 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7426 (mtt90) cc_final: 0.7170 (mtm180) REVERT: A 71 GLN cc_start: 0.6868 (tt0) cc_final: 0.5947 (mm110) REVERT: A 91 ASN cc_start: 0.8991 (m-40) cc_final: 0.8543 (m110) REVERT: E 19 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6612 (mm110) REVERT: E 34 ARG cc_start: 0.7427 (mtt90) cc_final: 0.6867 (mtm180) REVERT: E 44 MET cc_start: 0.7365 (mmm) cc_final: 0.6828 (mmm) REVERT: E 202 ARG cc_start: 0.7602 (mtt180) cc_final: 0.7284 (mtp-110) REVERT: E 306 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6940 (mp0) REVERT: E 324 GLU cc_start: 0.8100 (tp30) cc_final: 0.7745 (tm-30) REVERT: D 19 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6190 (mm110) REVERT: D 91 ASN cc_start: 0.8936 (m-40) cc_final: 0.8594 (m110) REVERT: D 149 LYS cc_start: 0.8471 (mttp) cc_final: 0.8196 (mttt) REVERT: D 202 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7328 (mtp-110) REVERT: D 245 TYR cc_start: 0.7434 (m-10) cc_final: 0.7177 (m-80) REVERT: D 306 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7242 (mp0) REVERT: D 316 GLN cc_start: 0.8330 (tm130) cc_final: 0.7704 (tt0) REVERT: B 32 LEU cc_start: 0.8479 (tp) cc_final: 0.8177 (tt) REVERT: B 36 LEU cc_start: 0.8705 (tp) cc_final: 0.8435 (mp) REVERT: B 173 ASN cc_start: 0.8153 (m-40) cc_final: 0.7895 (m-40) REVERT: C 34 ARG cc_start: 0.7727 (mtt90) cc_final: 0.7410 (mtm180) REVERT: C 168 ARG cc_start: 0.7294 (tmt90) cc_final: 0.6902 (tmm-80) REVERT: C 173 ASN cc_start: 0.7598 (m-40) cc_final: 0.7390 (m110) REVERT: C 202 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7166 (mtp-110) REVERT: C 282 PHE cc_start: 0.7935 (t80) cc_final: 0.7679 (t80) outliers start: 28 outliers final: 11 residues processed: 288 average time/residue: 0.2742 time to fit residues: 114.1665 Evaluate side-chains 235 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 177 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN A 267 HIS E 156 HIS E 204 ASN ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN B 91 ASN B 115 HIS ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.163208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145916 restraints weight = 30555.745| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.52 r_work: 0.3535 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14725 Z= 0.186 Angle : 0.603 8.917 19980 Z= 0.323 Chirality : 0.042 0.185 2170 Planarity : 0.004 0.057 2495 Dihedral : 4.147 19.020 1960 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.91 % Allowed : 13.55 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1710 helix: 1.16 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.13 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 182 HIS 0.002 0.001 HIS A 267 PHE 0.053 0.002 PHE E 42 TYR 0.025 0.002 TYR A 43 ARG 0.010 0.001 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.05610 ( 975) hydrogen bonds : angle 4.78328 ( 2815) covalent geometry : bond 0.00412 (14725) covalent geometry : angle 0.60315 (19980) *********************** 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 279 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7506 (mtt90) cc_final: 0.7248 (mtm180) REVERT: A 38 CYS cc_start: 0.7681 (p) cc_final: 0.7467 (p) REVERT: E 19 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6162 (mm110) REVERT: E 44 MET cc_start: 0.7047 (mmm) cc_final: 0.6791 (mmm) REVERT: E 324 GLU cc_start: 0.8257 (tp30) cc_final: 0.7915 (tm-30) REVERT: D 19 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6168 (mm110) REVERT: D 149 LYS cc_start: 0.8520 (mttp) cc_final: 0.8308 (mttt) REVERT: D 173 ASN cc_start: 0.7936 (m-40) cc_final: 0.7702 (m-40) REVERT: D 202 ARG cc_start: 0.7866 (mtt180) cc_final: 0.7465 (mtp-110) REVERT: D 218 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7496 (ttp80) REVERT: D 264 TYR cc_start: 0.6998 (m-10) cc_final: 0.6787 (m-10) REVERT: D 316 GLN cc_start: 0.8317 (tm130) cc_final: 0.8109 (tt0) REVERT: B 173 ASN cc_start: 0.8210 (m-40) cc_final: 0.7938 (m-40) REVERT: C 34 ARG cc_start: 0.7737 (mtt90) cc_final: 0.7514 (mtm180) REVERT: C 168 ARG cc_start: 0.7286 (tmt90) cc_final: 0.6866 (tmm-80) REVERT: C 202 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7260 (mtp-110) outliers start: 29 outliers final: 15 residues processed: 273 average time/residue: 0.2721 time to fit residues: 108.6447 Evaluate side-chains 232 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 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 23 LEU 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 7 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 6 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 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 HIS ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN E 204 ASN D 91 ASN ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN D 316 GLN B 96 GLN B 190 ASN B 204 ASN C 156 HIS C 173 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.162879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.142740 restraints weight = 41756.910| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.35 r_work: 0.3510 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14725 Z= 0.158 Angle : 0.577 11.087 19980 Z= 0.308 Chirality : 0.042 0.193 2170 Planarity : 0.004 0.049 2495 Dihedral : 4.049 20.203 1960 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.78 % Allowed : 14.34 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1710 helix: 1.20 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.16 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.002 0.001 HIS E 115 PHE 0.049 0.002 PHE E 42 TYR 0.024 0.002 TYR A 43 ARG 0.012 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 975) hydrogen bonds : angle 4.75207 ( 2815) covalent geometry : bond 0.00347 (14725) covalent geometry : angle 0.57689 (19980) *********************** 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 273 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7592 (mtp180) REVERT: A 203 ASP cc_start: 0.7312 (p0) cc_final: 0.6538 (m-30) REVERT: E 19 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6822 (pp30) REVERT: E 44 MET cc_start: 0.6769 (mmm) cc_final: 0.6452 (mmm) REVERT: E 264 TYR cc_start: 0.7195 (m-10) cc_final: 0.6870 (m-10) REVERT: E 274 PRO cc_start: 0.6261 (Cg_endo) cc_final: 0.6011 (Cg_exo) REVERT: E 324 GLU cc_start: 0.8182 (tp30) cc_final: 0.7907 (tm-30) REVERT: D 19 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6101 (mm110) REVERT: D 32 LEU cc_start: 0.8202 (tp) cc_final: 0.7942 (tt) REVERT: D 149 LYS cc_start: 0.8150 (mttp) cc_final: 0.7907 (mttt) REVERT: D 202 ARG cc_start: 0.7851 (mtt180) cc_final: 0.7441 (mtp-110) REVERT: D 218 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7398 (ttp80) REVERT: D 316 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8017 (tt0) REVERT: B 42 PHE cc_start: 0.7248 (m-80) cc_final: 0.6947 (m-80) REVERT: B 71 GLN cc_start: 0.7121 (tt0) cc_final: 0.6909 (tt0) REVERT: B 173 ASN cc_start: 0.8118 (m-40) cc_final: 0.7783 (m-40) REVERT: B 273 VAL cc_start: 0.6118 (t) cc_final: 0.5852 (p) REVERT: C 34 ARG cc_start: 0.7569 (mtt90) cc_final: 0.7126 (mtm180) REVERT: C 91 ASN cc_start: 0.8611 (m110) cc_final: 0.8246 (m110) REVERT: C 168 ARG cc_start: 0.7237 (tmt90) cc_final: 0.6696 (tmm-80) REVERT: C 202 ARG cc_start: 0.7719 (mtt180) cc_final: 0.7388 (mtp-110) outliers start: 27 outliers final: 17 residues processed: 265 average time/residue: 0.2474 time to fit residues: 97.7557 Evaluate side-chains 242 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 46 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 LEU 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 36 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 29 TYR 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 99 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 137 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN E 115 HIS E 204 ASN D 115 HIS ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN C 204 ASN C 293 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.158409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139592 restraints weight = 35307.038| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.96 r_work: 0.3487 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14725 Z= 0.200 Angle : 0.616 12.567 19980 Z= 0.327 Chirality : 0.043 0.203 2170 Planarity : 0.004 0.048 2495 Dihedral : 4.140 21.014 1960 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.11 % Allowed : 14.80 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1710 helix: 1.13 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.16 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 94 HIS 0.005 0.001 HIS E 115 PHE 0.049 0.002 PHE E 42 TYR 0.025 0.002 TYR A 43 ARG 0.012 0.001 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.05508 ( 975) hydrogen bonds : angle 4.79618 ( 2815) covalent geometry : bond 0.00454 (14725) covalent geometry : angle 0.61625 (19980) *********************** 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 269 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ASP cc_start: 0.7110 (p0) cc_final: 0.6527 (m-30) REVERT: E 19 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6813 (pp30) REVERT: E 32 LEU cc_start: 0.8112 (tp) cc_final: 0.7907 (tp) REVERT: E 44 MET cc_start: 0.6773 (mmm) cc_final: 0.6433 (mmm) REVERT: E 324 GLU cc_start: 0.8178 (tp30) cc_final: 0.7921 (tm-30) REVERT: D 19 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6078 (mm110) REVERT: D 32 LEU cc_start: 0.8242 (tp) cc_final: 0.7962 (tt) REVERT: D 149 LYS cc_start: 0.8190 (mttp) cc_final: 0.7874 (mttt) REVERT: D 202 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7458 (mtp-110) REVERT: D 218 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7396 (ttp80) REVERT: D 316 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7916 (tt0) REVERT: B 71 GLN cc_start: 0.7225 (tt0) cc_final: 0.6998 (tt0) REVERT: B 173 ASN cc_start: 0.8073 (m-40) cc_final: 0.7720 (m-40) REVERT: B 273 VAL cc_start: 0.6575 (t) cc_final: 0.6324 (p) REVERT: C 34 ARG cc_start: 0.7542 (mtt90) cc_final: 0.7103 (mtm180) REVERT: C 91 ASN cc_start: 0.8677 (m110) cc_final: 0.8278 (m110) REVERT: C 197 ARG cc_start: 0.8481 (ttp80) cc_final: 0.7940 (ttp80) REVERT: C 202 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7434 (mtp-110) outliers start: 32 outliers final: 21 residues processed: 262 average time/residue: 0.2564 time to fit residues: 100.5165 Evaluate side-chains 245 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 A residue 364 THR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 LEU 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 36 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 29 TYR 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 71 GLN 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 147 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS A 173 ASN ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 204 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.161601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.142187 restraints weight = 37478.727| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.12 r_work: 0.3513 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14725 Z= 0.153 Angle : 0.582 12.892 19980 Z= 0.309 Chirality : 0.042 0.212 2170 Planarity : 0.004 0.049 2495 Dihedral : 4.044 20.753 1960 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1710 helix: 1.21 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.21 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.002 0.001 HIS C 156 PHE 0.049 0.002 PHE B 42 TYR 0.025 0.002 TYR A 43 ARG 0.013 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.05187 ( 975) hydrogen bonds : angle 4.77924 ( 2815) covalent geometry : bond 0.00330 (14725) covalent geometry : angle 0.58177 (19980) *********************** 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 266 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7827 (mtp85) REVERT: A 202 ARG cc_start: 0.8062 (mtp85) cc_final: 0.7698 (mtp85) REVERT: A 203 ASP cc_start: 0.7242 (p0) cc_final: 0.6641 (m-30) REVERT: E 19 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6048 (mm110) REVERT: E 44 MET cc_start: 0.6760 (mmm) cc_final: 0.6422 (mmm) REVERT: E 324 GLU cc_start: 0.8016 (tp30) cc_final: 0.7759 (tm-30) REVERT: D 19 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6350 (mm110) REVERT: D 32 LEU cc_start: 0.8200 (tp) cc_final: 0.7896 (tt) REVERT: D 60 ARG cc_start: 0.7121 (mmp80) cc_final: 0.6910 (mmp80) REVERT: D 149 LYS cc_start: 0.8161 (mttp) cc_final: 0.7828 (mttt) REVERT: D 202 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7491 (mtp-110) REVERT: D 273 VAL cc_start: 0.6554 (t) cc_final: 0.6269 (p) REVERT: D 316 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7884 (tt0) REVERT: B 71 GLN cc_start: 0.7219 (tt0) cc_final: 0.7009 (tt0) REVERT: B 173 ASN cc_start: 0.8043 (m-40) cc_final: 0.7679 (m-40) REVERT: B 249 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7191 (mp) REVERT: B 273 VAL cc_start: 0.6528 (t) cc_final: 0.6289 (p) REVERT: C 32 LEU cc_start: 0.8329 (tp) cc_final: 0.8123 (tt) REVERT: C 34 ARG cc_start: 0.7538 (mtt90) cc_final: 0.7024 (mtm180) REVERT: C 44 MET cc_start: 0.7022 (mmm) cc_final: 0.6537 (mmp) REVERT: C 91 ASN cc_start: 0.8686 (m110) cc_final: 0.8265 (m110) REVERT: C 202 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7426 (mtp-110) outliers start: 29 outliers final: 18 residues processed: 263 average time/residue: 0.2635 time to fit residues: 102.3905 Evaluate side-chains 242 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 87 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN E 314 ASN ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 204 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141011 restraints weight = 39360.625| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.21 r_work: 0.3497 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14725 Z= 0.168 Angle : 0.598 13.111 19980 Z= 0.318 Chirality : 0.042 0.206 2170 Planarity : 0.004 0.043 2495 Dihedral : 4.063 21.237 1960 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.17 % Allowed : 15.13 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1710 helix: 1.19 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.21 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.003 0.001 HIS A 156 PHE 0.046 0.002 PHE B 42 TYR 0.025 0.002 TYR A 43 ARG 0.012 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.05247 ( 975) hydrogen bonds : angle 4.78500 ( 2815) covalent geometry : bond 0.00372 (14725) covalent geometry : angle 0.59797 (19980) *********************** 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 277 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7850 (mtp85) REVERT: A 29 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: A 34 ARG cc_start: 0.7353 (mtt90) cc_final: 0.6794 (mtm180) REVERT: A 202 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7723 (mtp85) REVERT: A 203 ASP cc_start: 0.7294 (p0) cc_final: 0.6725 (m-30) REVERT: A 249 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7239 (mp) REVERT: E 8 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7829 (mtp-110) REVERT: E 19 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6766 (pp30) REVERT: E 32 LEU cc_start: 0.8095 (tp) cc_final: 0.7891 (tp) REVERT: E 44 MET cc_start: 0.6816 (mmm) cc_final: 0.6466 (mmm) REVERT: E 314 ASN cc_start: 0.8079 (m-40) cc_final: 0.7845 (m-40) REVERT: E 324 GLU cc_start: 0.8105 (tp30) cc_final: 0.7867 (tm-30) REVERT: D 19 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6353 (mm110) REVERT: D 32 LEU cc_start: 0.8227 (tp) cc_final: 0.7931 (tt) REVERT: D 42 PHE cc_start: 0.7370 (m-80) cc_final: 0.7078 (m-80) REVERT: D 60 ARG cc_start: 0.6993 (mmp80) cc_final: 0.6793 (mmp80) REVERT: D 149 LYS cc_start: 0.8209 (mttp) cc_final: 0.7896 (mttt) REVERT: D 202 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7587 (mtp-110) REVERT: D 273 VAL cc_start: 0.6652 (t) cc_final: 0.6323 (p) REVERT: D 316 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7866 (tt0) REVERT: B 71 GLN cc_start: 0.7272 (tt0) cc_final: 0.7053 (tt0) REVERT: B 173 ASN cc_start: 0.8042 (m-40) cc_final: 0.7664 (m-40) REVERT: B 249 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7198 (mp) REVERT: C 32 LEU cc_start: 0.8377 (tp) cc_final: 0.8159 (tt) REVERT: C 34 ARG cc_start: 0.7418 (mtt90) cc_final: 0.7037 (mtm180) REVERT: C 44 MET cc_start: 0.7100 (mmm) cc_final: 0.6591 (mmp) REVERT: C 202 ARG cc_start: 0.7755 (mtt180) cc_final: 0.7487 (mtp-110) REVERT: C 316 GLN cc_start: 0.8264 (tp40) cc_final: 0.7707 (tt0) outliers start: 33 outliers final: 22 residues processed: 268 average time/residue: 0.2511 time to fit residues: 99.2223 Evaluate side-chains 260 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 36 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 307 THR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 214 LEU 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 36 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 32 LEU 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 Chi-restraints excluded: chain C residue 272 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 128 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 94 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS D 173 ASN C 115 HIS C 204 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145590 restraints weight = 30285.528| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.76 r_work: 0.3576 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14725 Z= 0.139 Angle : 0.574 13.406 19980 Z= 0.305 Chirality : 0.041 0.221 2170 Planarity : 0.004 0.039 2495 Dihedral : 3.982 20.514 1960 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.71 % Allowed : 16.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1710 helix: 1.30 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.21 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.002 0.001 HIS C 156 PHE 0.045 0.002 PHE B 42 TYR 0.023 0.002 TYR A 43 ARG 0.011 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.05000 ( 975) hydrogen bonds : angle 4.73577 ( 2815) covalent geometry : bond 0.00291 (14725) covalent geometry : angle 0.57420 (19980) *********************** 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 276 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7923 (mtp85) REVERT: A 34 ARG cc_start: 0.7390 (mtt90) cc_final: 0.6840 (mtm180) REVERT: A 202 ARG cc_start: 0.7971 (mtp85) cc_final: 0.7658 (mtp85) REVERT: A 203 ASP cc_start: 0.7252 (p0) cc_final: 0.6793 (m-30) REVERT: A 249 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7350 (mp) REVERT: E 19 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6049 (mm110) REVERT: E 44 MET cc_start: 0.6870 (mmm) cc_final: 0.6535 (mmm) REVERT: E 324 GLU cc_start: 0.8065 (tp30) cc_final: 0.7843 (tm-30) REVERT: D 19 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6560 (mm110) REVERT: D 32 LEU cc_start: 0.8249 (tp) cc_final: 0.7985 (tt) REVERT: D 60 ARG cc_start: 0.7019 (mmp80) cc_final: 0.6806 (mmp80) REVERT: D 149 LYS cc_start: 0.8266 (mttp) cc_final: 0.7937 (mttt) REVERT: D 273 VAL cc_start: 0.6579 (t) cc_final: 0.6237 (p) REVERT: D 316 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7872 (tt0) REVERT: D 339 ASP cc_start: 0.6269 (m-30) cc_final: 0.6042 (m-30) REVERT: B 71 GLN cc_start: 0.7422 (tt0) cc_final: 0.7219 (tt0) REVERT: B 173 ASN cc_start: 0.8113 (m-40) cc_final: 0.7737 (m-40) REVERT: B 249 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7147 (mp) REVERT: C 32 LEU cc_start: 0.8398 (tp) cc_final: 0.8188 (tt) REVERT: C 34 ARG cc_start: 0.7495 (mtt90) cc_final: 0.7078 (mtm180) REVERT: C 44 MET cc_start: 0.7111 (mmm) cc_final: 0.6626 (mmp) REVERT: C 181 TYR cc_start: 0.8518 (p90) cc_final: 0.7660 (p90) REVERT: C 316 GLN cc_start: 0.8253 (tp40) cc_final: 0.7740 (tt0) outliers start: 26 outliers final: 18 residues processed: 271 average time/residue: 0.2598 time to fit residues: 103.7988 Evaluate side-chains 252 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 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 307 THR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 214 LEU 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 36 LEU Chi-restraints excluded: chain D residue 153 THR 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 Chi-restraints excluded: chain C residue 272 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 137 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN D 173 ASN D 204 ASN ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.144101 restraints weight = 33029.270| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.09 r_work: 0.3549 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4062 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= 0.149 Angle : 0.600 13.186 19980 Z= 0.316 Chirality : 0.041 0.211 2170 Planarity : 0.004 0.039 2495 Dihedral : 3.987 20.426 1960 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.58 % Allowed : 16.71 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1710 helix: 1.36 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.32 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.003 0.001 HIS D 156 PHE 0.049 0.002 PHE B 42 TYR 0.025 0.002 TYR A 43 ARG 0.011 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 975) hydrogen bonds : angle 4.74328 ( 2815) covalent geometry : bond 0.00324 (14725) covalent geometry : angle 0.59995 (19980) *********************** 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 256 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7878 (mtp85) REVERT: A 34 ARG cc_start: 0.7270 (mtt90) cc_final: 0.6674 (mtm180) REVERT: A 249 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7214 (mp) REVERT: E 44 MET cc_start: 0.6793 (mmm) cc_final: 0.6471 (mmm) REVERT: E 324 GLU cc_start: 0.7991 (tp30) cc_final: 0.7762 (tm-30) REVERT: D 19 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6384 (mm110) REVERT: D 32 LEU cc_start: 0.8175 (tp) cc_final: 0.7895 (tt) REVERT: D 60 ARG cc_start: 0.6951 (mmp80) cc_final: 0.6711 (mmp80) REVERT: D 149 LYS cc_start: 0.8120 (mttp) cc_final: 0.7819 (mttt) REVERT: D 316 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7852 (tt0) REVERT: D 339 ASP cc_start: 0.6301 (m-30) cc_final: 0.6099 (m-30) REVERT: B 71 GLN cc_start: 0.7367 (tt0) cc_final: 0.7158 (tt0) REVERT: B 173 ASN cc_start: 0.8103 (m-40) cc_final: 0.7726 (m-40) REVERT: B 249 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7127 (mp) REVERT: B 282 PHE cc_start: 0.7998 (t80) cc_final: 0.7437 (t80) REVERT: C 13 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7604 (mtm110) REVERT: C 32 LEU cc_start: 0.8324 (tp) cc_final: 0.8113 (tt) REVERT: C 34 ARG cc_start: 0.7423 (mtt90) cc_final: 0.6972 (mtm180) REVERT: C 44 MET cc_start: 0.7050 (mmm) cc_final: 0.6562 (mmp) REVERT: C 316 GLN cc_start: 0.8267 (tp40) cc_final: 0.7686 (tt0) outliers start: 24 outliers final: 18 residues processed: 251 average time/residue: 0.2614 time to fit residues: 97.3619 Evaluate side-chains 245 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 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 307 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 177 SER 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 36 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain B residue 23 LEU 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 214 LEU Chi-restraints excluded: chain C residue 272 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 128 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 83 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 138 optimal weight: 0.0770 chunk 100 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 139 optimal weight: 0.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN 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 = 0.3931 r_free = 0.3931 target = 0.167090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147020 restraints weight = 37937.583| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.42 r_work: 0.3571 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14725 Z= 0.130 Angle : 0.577 13.217 19980 Z= 0.304 Chirality : 0.041 0.222 2170 Planarity : 0.004 0.036 2495 Dihedral : 3.908 19.478 1960 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.18 % Allowed : 16.97 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1710 helix: 1.47 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.27 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.002 0.001 HIS D 156 PHE 0.047 0.002 PHE B 42 TYR 0.026 0.002 TYR B 85 ARG 0.010 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.04832 ( 975) hydrogen bonds : angle 4.67649 ( 2815) covalent geometry : bond 0.00267 (14725) covalent geometry : angle 0.57676 (19980) ********************** 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 269 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 251 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7109 (mtt90) cc_final: 0.6558 (mtm180) REVERT: A 306 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6559 (mm-30) REVERT: E 34 ARG cc_start: 0.6913 (mtt90) cc_final: 0.6371 (mtm180) REVERT: E 44 MET cc_start: 0.6774 (mmm) cc_final: 0.6452 (mmm) REVERT: E 324 GLU cc_start: 0.8008 (tp30) cc_final: 0.7786 (tm-30) REVERT: D 19 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6380 (mm110) REVERT: D 32 LEU cc_start: 0.8100 (tp) cc_final: 0.7836 (tt) REVERT: D 149 LYS cc_start: 0.8122 (mttp) cc_final: 0.7837 (mttt) REVERT: D 316 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7835 (tt0) REVERT: D 339 ASP cc_start: 0.6277 (m-30) cc_final: 0.6076 (m-30) REVERT: B 173 ASN cc_start: 0.8113 (m-40) cc_final: 0.7733 (m-40) REVERT: B 249 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6970 (mp) REVERT: B 282 PHE cc_start: 0.7957 (t80) cc_final: 0.7496 (t80) REVERT: C 34 ARG cc_start: 0.7300 (mtt90) cc_final: 0.6911 (mtm180) REVERT: C 44 MET cc_start: 0.7014 (mmm) cc_final: 0.6559 (mmp) REVERT: C 95 SER cc_start: 0.8141 (m) cc_final: 0.7883 (m) REVERT: C 181 TYR cc_start: 0.8486 (p90) cc_final: 0.7596 (p90) REVERT: C 316 GLN cc_start: 0.8269 (tp40) cc_final: 0.7670 (tt0) outliers start: 18 outliers final: 15 residues processed: 264 average time/residue: 0.2883 time to fit residues: 111.3383 Evaluate side-chains 244 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 46 LEU 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 36 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain B residue 23 LEU 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 C residue 214 LEU Chi-restraints excluded: chain C residue 272 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 38 optimal weight: 5.9990 chunk 100 optimal weight: 0.0770 chunk 56 optimal weight: 0.0980 chunk 150 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 chunk 142 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN D 173 ASN B 204 ASN ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.166868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148863 restraints weight = 32417.640| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.85 r_work: 0.3602 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4290 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= 0.133 Angle : 0.605 15.191 19980 Z= 0.312 Chirality : 0.041 0.207 2170 Planarity : 0.004 0.036 2495 Dihedral : 3.907 19.206 1960 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.12 % Allowed : 17.70 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.20), residues: 1710 helix: 1.46 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.21 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.002 0.001 HIS D 156 PHE 0.047 0.002 PHE B 42 TYR 0.038 0.002 TYR A 85 ARG 0.010 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.04841 ( 975) hydrogen bonds : angle 4.67466 ( 2815) covalent geometry : bond 0.00279 (14725) covalent geometry : angle 0.60550 (19980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7615.76 seconds wall clock time: 133 minutes 50.90 seconds (8030.90 seconds total)