Starting phenix.real_space_refine on Tue Feb 3 19:59:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6e_49059/02_2026/9n6e_49059_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6e_49059/02_2026/9n6e_49059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n6e_49059/02_2026/9n6e_49059_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6e_49059/02_2026/9n6e_49059_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n6e_49059/02_2026/9n6e_49059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6e_49059/02_2026/9n6e_49059.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4138 2.51 5 N 1105 2.21 5 O 1258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6534 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 925 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "B" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 823 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "I" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1250 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 1.65, per 1000 atoms: 0.25 Number of scatterers: 6534 At special positions: 0 Unit cell: (86.2225, 95.6975, 117.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1258 8.00 N 1105 7.00 C 4138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 33 " distance=2.04 Simple disulfide: pdb=" SG CYS I 114 " - pdb=" SG CYS I 132 " distance=2.05 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 125 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 238.9 milliseconds 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1518 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 18 sheets defined 8.2% alpha, 43.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.024A pdb=" N VAL B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'I' and resid 47 through 69 Processing helix chain 'I' and resid 69 through 76 Processing helix chain 'I' and resid 137 through 145 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.819A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.619A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.730A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.544A pdb=" N LEU C 82C" --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER C 17 " --> pdb=" O ASP C 82A" (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP C 82A" --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG C 19 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLN C 81 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER C 21 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE C 79 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLU C 23 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR C 77 " --> pdb=" O GLU C 23 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.535A pdb=" N THR C 110 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN C 95 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLY C 33 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.535A pdb=" N THR C 110 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.763A pdb=" N ALA D 84 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.763A pdb=" N ALA D 84 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.819A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.722A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'I' and resid 8 through 14 removed outlier: 3.538A pdb=" N LYS I 24 " --> pdb=" O THR I 32 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR I 32 " --> pdb=" O LYS I 24 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 126 through 127 Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.152A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.152A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 663 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: 0.91 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1511 1.33 - 1.45: 1713 1.45 - 1.58: 3413 1.58 - 1.71: 0 1.71 - 1.83: 48 Bond restraints: 6685 Sorted by residual: bond pdb=" CB HIS A 35 " pdb=" CG HIS A 35 " ideal model delta sigma weight residual 1.497 1.456 0.041 1.40e-02 5.10e+03 8.74e+00 bond pdb=" N PRO B 8 " pdb=" CD PRO B 8 " ideal model delta sigma weight residual 1.473 1.434 0.039 1.40e-02 5.10e+03 7.73e+00 bond pdb=" CB HIS H 35 " pdb=" CG HIS H 35 " ideal model delta sigma weight residual 1.497 1.458 0.039 1.40e-02 5.10e+03 7.56e+00 bond pdb=" CD GLU L 55 " pdb=" OE1 GLU L 55 " ideal model delta sigma weight residual 1.249 1.199 0.050 1.90e-02 2.77e+03 6.99e+00 bond pdb=" NE ARG L 96 " pdb=" CZ ARG L 96 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.10e-02 8.26e+03 6.72e+00 ... (remaining 6680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 8218 2.09 - 4.19: 698 4.19 - 6.28: 107 6.28 - 8.37: 19 8.37 - 10.46: 2 Bond angle restraints: 9044 Sorted by residual: angle pdb=" C GLY A 100A" pdb=" N PRO A 100B" pdb=" CA PRO A 100B" ideal model delta sigma weight residual 119.78 129.37 -9.59 1.03e+00 9.43e-01 8.67e+01 angle pdb=" C THR I 128 " pdb=" N PRO I 129 " pdb=" CA PRO I 129 " ideal model delta sigma weight residual 119.56 127.30 -7.74 1.02e+00 9.61e-01 5.76e+01 angle pdb=" C GLY H 100A" pdb=" N PRO H 100B" pdb=" CA PRO H 100B" ideal model delta sigma weight residual 119.78 127.56 -7.78 1.03e+00 9.43e-01 5.71e+01 angle pdb=" C ALA D 43 " pdb=" N PRO D 44 " pdb=" CA PRO D 44 " ideal model delta sigma weight residual 120.03 127.13 -7.10 9.90e-01 1.02e+00 5.14e+01 angle pdb=" C ASP I 47 " pdb=" N PRO I 48 " pdb=" CA PRO I 48 " ideal model delta sigma weight residual 119.56 126.69 -7.13 1.02e+00 9.61e-01 4.88e+01 ... (remaining 9039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3808 17.81 - 35.62: 105 35.62 - 53.43: 24 53.43 - 71.24: 17 71.24 - 89.05: 12 Dihedral angle restraints: 3966 sinusoidal: 1584 harmonic: 2382 Sorted by residual: dihedral pdb=" CA LEU D 54 " pdb=" C LEU D 54 " pdb=" N GLU D 55 " pdb=" CA GLU D 55 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA LYS A 75 " pdb=" C LYS A 75 " pdb=" N ASN A 76 " pdb=" CA ASN A 76 " ideal model delta harmonic sigma weight residual 180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ALA C 88 " pdb=" C ALA C 88 " pdb=" N VAL C 89 " pdb=" CA VAL C 89 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 3963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 609 0.055 - 0.110: 301 0.110 - 0.165: 57 0.165 - 0.219: 8 0.219 - 0.274: 2 Chirality restraints: 977 Sorted by residual: chirality pdb=" CA SER L 7 " pdb=" N SER L 7 " pdb=" C SER L 7 " pdb=" CB SER L 7 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA TYR C 97 " pdb=" N TYR C 97 " pdb=" C TYR C 97 " pdb=" CB TYR C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA SER B 7 " pdb=" N SER B 7 " pdb=" C SER B 7 " pdb=" CB SER B 7 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 974 not shown) Planarity restraints: 1152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 32 " 0.039 2.00e-02 2.50e+03 2.02e-02 8.17e+00 pdb=" CG TYR C 32 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 32 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 32 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 32 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 32 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 32 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 32 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 97 " 0.033 2.00e-02 2.50e+03 1.93e-02 7.46e+00 pdb=" CG TYR A 97 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 97 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 97 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 97 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 97 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 97 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 97 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 85 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C GLU C 85 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU C 85 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP C 86 " -0.013 2.00e-02 2.50e+03 ... (remaining 1149 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1460 2.78 - 3.31: 5472 3.31 - 3.84: 10390 3.84 - 4.37: 11984 4.37 - 4.90: 21154 Nonbonded interactions: 50460 Sorted by model distance: nonbonded pdb=" CB ALA B 34 " pdb=" OH TYR B 91 " model vdw 2.251 3.460 nonbonded pdb=" CB ALA B 34 " pdb=" CE2 TYR B 91 " model vdw 2.312 3.760 nonbonded pdb=" OG SER A 7 " pdb=" OG SER A 21 " model vdw 2.426 3.040 nonbonded pdb=" O CYS A 22 " pdb=" OG1 THR A 77 " model vdw 2.479 3.040 nonbonded pdb=" OD1 ASP C 61 " pdb=" N SER C 62 " model vdw 2.494 3.120 ... (remaining 50455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 2 through 111) selection = (chain 'H' and resid 2 through 111) } ncs_group { reference = (chain 'B' and resid 2 through 106) selection = (chain 'D' and resid 2 through 106) selection = (chain 'L' and resid 2 through 106) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.350 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4359 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 : 0.013 0.075 6694 Z= 0.670 Angle : 1.291 10.464 9062 Z= 0.882 Chirality : 0.062 0.274 977 Planarity : 0.006 0.021 1152 Dihedral : 11.641 89.050 2421 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.31), residues: 816 helix: 0.46 (0.70), residues: 39 sheet: 1.34 (0.26), residues: 359 loop : 2.36 (0.35), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 31 TYR 0.039 0.005 TYR C 32 PHE 0.018 0.004 PHE H 67 TRP 0.023 0.004 TRP A 103 HIS 0.001 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.01251 ( 6685) covalent geometry : angle 1.28794 ( 9044) SS BOND : bond 0.00935 ( 9) SS BOND : angle 2.29999 ( 18) hydrogen bonds : bond 0.19231 ( 256) hydrogen bonds : angle 7.92952 ( 663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 SER cc_start: 0.6552 (m) cc_final: 0.6241 (t) REVERT: B 35 TRP cc_start: 0.6137 (m100) cc_final: 0.5788 (m100) REVERT: B 42 LYS cc_start: 0.6618 (mttt) cc_final: 0.6256 (tttp) REVERT: H 47 TRP cc_start: 0.3862 (t60) cc_final: 0.3216 (t60) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.0947 time to fit residues: 23.9225 Evaluate side-chains 102 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 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 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN B 89 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN H 1 GLN I 45 ASN L 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.233856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.203559 restraints weight = 7522.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.208758 restraints weight = 4564.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.212203 restraints weight = 3196.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.214576 restraints weight = 2472.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.216474 restraints weight = 2052.475| |-----------------------------------------------------------------------------| r_work (final): 0.4619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6694 Z= 0.221 Angle : 0.819 8.402 9062 Z= 0.438 Chirality : 0.050 0.141 977 Planarity : 0.007 0.053 1152 Dihedral : 5.956 41.124 905 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.92 % Favored : 95.96 % Rotamer: Outliers : 2.92 % Allowed : 7.64 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.30), residues: 816 helix: 0.87 (0.73), residues: 40 sheet: 1.12 (0.27), residues: 350 loop : 0.78 (0.34), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 66 TYR 0.024 0.003 TYR C 97 PHE 0.028 0.003 PHE H 29 TRP 0.025 0.003 TRP H 52 HIS 0.008 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 6685) covalent geometry : angle 0.81301 ( 9044) SS BOND : bond 0.00872 ( 9) SS BOND : angle 2.33004 ( 18) hydrogen bonds : bond 0.04262 ( 256) hydrogen bonds : angle 6.02609 ( 663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.257 Fit side-chains REVERT: B 42 LYS cc_start: 0.6840 (mttt) cc_final: 0.6591 (tttp) REVERT: B 91 TYR cc_start: 0.5142 (m-80) cc_final: 0.4397 (m-80) REVERT: C 102 TYR cc_start: 0.5839 (m-80) cc_final: 0.5478 (m-80) REVERT: D 24 ARG cc_start: 0.7262 (ttm110) cc_final: 0.7039 (ttm-80) REVERT: H 74 SER cc_start: 0.6597 (p) cc_final: 0.6392 (m) REVERT: H 83 ARG cc_start: 0.5393 (OUTLIER) cc_final: 0.4896 (ptp-170) REVERT: I 116 MET cc_start: 0.6317 (mmm) cc_final: 0.5950 (mmm) outliers start: 21 outliers final: 12 residues processed: 184 average time/residue: 0.0683 time to fit residues: 16.7360 Evaluate side-chains 139 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS D 70 HIS H 81 GLN I 133 ASN I 135 ASN L 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.226321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.194413 restraints weight = 7740.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.199366 restraints weight = 4902.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.202673 restraints weight = 3555.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.204722 restraints weight = 2824.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.206402 restraints weight = 2406.797| |-----------------------------------------------------------------------------| r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.8112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6694 Z= 0.180 Angle : 0.694 10.078 9062 Z= 0.375 Chirality : 0.047 0.260 977 Planarity : 0.005 0.047 1152 Dihedral : 5.170 18.502 905 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.90 % Favored : 94.98 % Rotamer: Outliers : 4.03 % Allowed : 12.78 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.31), residues: 816 helix: 1.20 (0.70), residues: 40 sheet: 0.94 (0.27), residues: 364 loop : 0.60 (0.34), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 96 TYR 0.018 0.002 TYR L 91 PHE 0.025 0.003 PHE H 52A TRP 0.031 0.003 TRP B 35 HIS 0.004 0.002 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6685) covalent geometry : angle 0.69063 ( 9044) SS BOND : bond 0.00480 ( 9) SS BOND : angle 1.77253 ( 18) hydrogen bonds : bond 0.04287 ( 256) hydrogen bonds : angle 5.50668 ( 663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: H 83 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.4858 (ptp-170) REVERT: I 116 MET cc_start: 0.7158 (mmm) cc_final: 0.6679 (mmm) REVERT: I 143 LYS cc_start: 0.6009 (mmtt) cc_final: 0.5523 (pttt) REVERT: L 42 LYS cc_start: 0.6564 (tppt) cc_final: 0.6329 (mtpp) outliers start: 29 outliers final: 21 residues processed: 168 average time/residue: 0.0716 time to fit residues: 15.8768 Evaluate side-chains 153 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 0.0170 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.0670 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN C 81 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** I 133 ASN ** 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 = 0.4692 r_free = 0.4692 target = 0.226940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.194228 restraints weight = 7916.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.199259 restraints weight = 5073.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.202664 restraints weight = 3711.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.204702 restraints weight = 2973.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.206283 restraints weight = 2549.565| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.9163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6694 Z= 0.136 Angle : 0.646 8.610 9062 Z= 0.340 Chirality : 0.045 0.147 977 Planarity : 0.005 0.041 1152 Dihedral : 5.048 26.326 905 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.66 % Favored : 95.22 % Rotamer: Outliers : 4.17 % Allowed : 12.78 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.30), residues: 816 helix: 1.25 (0.70), residues: 40 sheet: 0.98 (0.28), residues: 342 loop : 0.42 (0.33), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 96 TYR 0.013 0.002 TYR A 91 PHE 0.021 0.002 PHE C 100C TRP 0.019 0.002 TRP C 103 HIS 0.002 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6685) covalent geometry : angle 0.64153 ( 9044) SS BOND : bond 0.00334 ( 9) SS BOND : angle 1.76908 ( 18) hydrogen bonds : bond 0.03343 ( 256) hydrogen bonds : angle 5.17627 ( 663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.244 Fit side-chains REVERT: A 80 MET cc_start: 0.5887 (tpp) cc_final: 0.5484 (tpt) REVERT: A 81 GLN cc_start: 0.3743 (tp40) cc_final: 0.3027 (tp40) REVERT: B 100 GLN cc_start: 0.6452 (tp-100) cc_final: 0.6237 (mp10) REVERT: B 105 GLU cc_start: 0.7687 (mp0) cc_final: 0.7354 (mp0) REVERT: C 82 SER cc_start: 0.6715 (m) cc_final: 0.5430 (p) REVERT: D 45 LYS cc_start: 0.7126 (mtpt) cc_final: 0.6780 (mtmm) REVERT: H 83 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.5597 (ptp-170) REVERT: I 89 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7074 (pt) REVERT: L 42 LYS cc_start: 0.6478 (tppt) cc_final: 0.6272 (mtpp) outliers start: 30 outliers final: 21 residues processed: 176 average time/residue: 0.0745 time to fit residues: 17.3308 Evaluate side-chains 151 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0070 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN I 133 ASN L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.212528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.179158 restraints weight = 7885.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.183795 restraints weight = 5123.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.186892 restraints weight = 3780.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.188812 restraints weight = 3065.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.190197 restraints weight = 2654.333| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 1.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6694 Z= 0.205 Angle : 0.752 8.962 9062 Z= 0.403 Chirality : 0.048 0.145 977 Planarity : 0.006 0.055 1152 Dihedral : 5.581 29.003 905 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.99 % Favored : 92.89 % Rotamer: Outliers : 5.56 % Allowed : 13.89 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.31), residues: 816 helix: 1.34 (0.68), residues: 40 sheet: 0.61 (0.27), residues: 370 loop : 0.00 (0.34), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 94 TYR 0.028 0.003 TYR H 91 PHE 0.032 0.003 PHE A 96 TRP 0.025 0.003 TRP C 103 HIS 0.006 0.002 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 6685) covalent geometry : angle 0.74857 ( 9044) SS BOND : bond 0.00852 ( 9) SS BOND : angle 1.80961 ( 18) hydrogen bonds : bond 0.04194 ( 256) hydrogen bonds : angle 5.66827 ( 663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.6157 (tpp) cc_final: 0.5877 (tpt) REVERT: A 91 TYR cc_start: 0.8135 (m-80) cc_final: 0.7862 (m-80) REVERT: B 30 SER cc_start: 0.9096 (m) cc_final: 0.8841 (p) REVERT: D 45 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7388 (mttp) REVERT: H 83 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5094 (ptp-170) REVERT: I 76 LEU cc_start: 0.7717 (mt) cc_final: 0.7460 (tp) REVERT: L 42 LYS cc_start: 0.7365 (tppt) cc_final: 0.7121 (mttm) outliers start: 40 outliers final: 35 residues processed: 177 average time/residue: 0.0858 time to fit residues: 19.9605 Evaluate side-chains 163 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS B 89 GLN H 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.219733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.186756 restraints weight = 7962.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.189960 restraints weight = 5726.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.191682 restraints weight = 4322.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.192058 restraints weight = 3852.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.192540 restraints weight = 3600.876| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 1.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6694 Z= 0.157 Angle : 0.664 8.871 9062 Z= 0.350 Chirality : 0.045 0.143 977 Planarity : 0.005 0.069 1152 Dihedral : 5.137 19.881 905 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.76 % Favored : 94.12 % Rotamer: Outliers : 5.69 % Allowed : 16.81 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.30), residues: 816 helix: 1.67 (0.65), residues: 40 sheet: 0.76 (0.28), residues: 341 loop : -0.21 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 61 TYR 0.013 0.002 TYR C 91 PHE 0.023 0.002 PHE C 100C TRP 0.016 0.002 TRP C 103 HIS 0.004 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6685) covalent geometry : angle 0.66301 ( 9044) SS BOND : bond 0.00469 ( 9) SS BOND : angle 1.15623 ( 18) hydrogen bonds : bond 0.03394 ( 256) hydrogen bonds : angle 5.26943 ( 663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: B 30 SER cc_start: 0.9090 (m) cc_final: 0.8846 (p) REVERT: H 83 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.5174 (ptp-170) outliers start: 41 outliers final: 34 residues processed: 159 average time/residue: 0.0893 time to fit residues: 18.7018 Evaluate side-chains 153 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN H 1 GLN H 35 HIS L 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.210254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.174932 restraints weight = 7855.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.179225 restraints weight = 5344.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182056 restraints weight = 4081.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.183690 restraints weight = 3406.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.185063 restraints weight = 3033.109| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 1.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6694 Z= 0.225 Angle : 0.737 8.605 9062 Z= 0.392 Chirality : 0.047 0.133 977 Planarity : 0.006 0.064 1152 Dihedral : 5.482 20.885 905 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.84 % Favored : 92.03 % Rotamer: Outliers : 6.81 % Allowed : 17.08 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.31), residues: 816 helix: 1.74 (0.64), residues: 40 sheet: 0.41 (0.27), residues: 363 loop : -0.51 (0.34), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 61 TYR 0.018 0.002 TYR B 36 PHE 0.022 0.003 PHE C 100C TRP 0.018 0.002 TRP C 103 HIS 0.007 0.002 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 6685) covalent geometry : angle 0.73459 ( 9044) SS BOND : bond 0.00472 ( 9) SS BOND : angle 1.46045 ( 18) hydrogen bonds : bond 0.03915 ( 256) hydrogen bonds : angle 5.70954 ( 663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 0.202 Fit side-chains REVERT: A 91 TYR cc_start: 0.8165 (m-80) cc_final: 0.7801 (m-80) REVERT: C 39 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: D 18 ARG cc_start: 0.7171 (mmm160) cc_final: 0.6939 (mmt180) REVERT: H 52 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.6237 (t80) REVERT: H 83 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5250 (ptp-170) REVERT: I 66 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6914 (mp) REVERT: I 116 MET cc_start: 0.7519 (mtt) cc_final: 0.7220 (mtt) outliers start: 49 outliers final: 34 residues processed: 173 average time/residue: 0.0966 time to fit residues: 21.5300 Evaluate side-chains 162 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.210804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.174526 restraints weight = 7969.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.179106 restraints weight = 5303.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.182176 restraints weight = 4020.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.184030 restraints weight = 3327.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.185565 restraints weight = 2933.303| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 1.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6694 Z= 0.193 Angle : 0.725 9.543 9062 Z= 0.381 Chirality : 0.046 0.169 977 Planarity : 0.005 0.069 1152 Dihedral : 5.410 25.355 905 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.62 % Favored : 93.26 % Rotamer: Outliers : 6.11 % Allowed : 18.61 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.30), residues: 816 helix: 2.00 (0.66), residues: 40 sheet: 0.26 (0.27), residues: 367 loop : -0.69 (0.34), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 31 TYR 0.016 0.002 TYR L 91 PHE 0.025 0.003 PHE C 100C TRP 0.014 0.002 TRP C 103 HIS 0.005 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 6685) covalent geometry : angle 0.71872 ( 9044) SS BOND : bond 0.00652 ( 9) SS BOND : angle 2.28478 ( 18) hydrogen bonds : bond 0.03625 ( 256) hydrogen bonds : angle 5.53894 ( 663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.204 Fit side-chains REVERT: A 91 TYR cc_start: 0.8127 (m-80) cc_final: 0.7897 (m-80) REVERT: C 39 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.7058 (tt0) REVERT: D 18 ARG cc_start: 0.7165 (mmm160) cc_final: 0.6953 (mmt180) REVERT: H 52 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6168 (t80) REVERT: H 82 SER cc_start: 0.8399 (m) cc_final: 0.8055 (t) REVERT: H 83 ARG cc_start: 0.6227 (OUTLIER) cc_final: 0.5748 (ptp-170) REVERT: L 92 THR cc_start: 0.8777 (t) cc_final: 0.8479 (t) outliers start: 44 outliers final: 33 residues processed: 164 average time/residue: 0.0949 time to fit residues: 20.0223 Evaluate side-chains 166 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.0370 chunk 33 optimal weight: 7.9990 chunk 17 optimal weight: 0.0570 chunk 52 optimal weight: 0.0970 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.217558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.182131 restraints weight = 7992.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.186916 restraints weight = 5207.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.190107 restraints weight = 3887.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.192115 restraints weight = 3176.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.193308 restraints weight = 2753.944| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 1.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6694 Z= 0.127 Angle : 0.650 8.229 9062 Z= 0.340 Chirality : 0.044 0.155 977 Planarity : 0.005 0.055 1152 Dihedral : 5.007 22.096 905 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.37 % Favored : 93.50 % Rotamer: Outliers : 4.58 % Allowed : 19.72 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.30), residues: 816 helix: 2.11 (0.67), residues: 40 sheet: 0.47 (0.28), residues: 342 loop : -0.63 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 31 TYR 0.013 0.001 TYR L 91 PHE 0.024 0.002 PHE C 100C TRP 0.015 0.001 TRP H 47 HIS 0.006 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6685) covalent geometry : angle 0.64536 ( 9044) SS BOND : bond 0.00486 ( 9) SS BOND : angle 1.83661 ( 18) hydrogen bonds : bond 0.03120 ( 256) hydrogen bonds : angle 5.03656 ( 663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.267 Fit side-chains REVERT: A 21 SER cc_start: 0.8042 (m) cc_final: 0.7837 (p) REVERT: A 47 TRP cc_start: 0.7229 (t60) cc_final: 0.6983 (t60) REVERT: C 39 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: C 79 PHE cc_start: 0.7590 (m-10) cc_final: 0.7238 (m-10) REVERT: D 18 ARG cc_start: 0.7206 (mmm160) cc_final: 0.6949 (mmt180) REVERT: H 53 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6580 (t0) REVERT: H 83 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5793 (mpt-90) REVERT: L 92 THR cc_start: 0.8832 (t) cc_final: 0.8593 (t) outliers start: 33 outliers final: 27 residues processed: 164 average time/residue: 0.0910 time to fit residues: 19.2313 Evaluate side-chains 167 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 48 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 6 GLN D 37 GLN I 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.206458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.171000 restraints weight = 7889.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.175094 restraints weight = 5425.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.177349 restraints weight = 4214.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.179463 restraints weight = 3583.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.180562 restraints weight = 3179.601| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 1.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 6694 Z= 0.247 Angle : 0.766 9.160 9062 Z= 0.404 Chirality : 0.048 0.227 977 Planarity : 0.006 0.078 1152 Dihedral : 5.525 23.617 905 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.97 % Favored : 91.91 % Rotamer: Outliers : 4.44 % Allowed : 20.56 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.30), residues: 816 helix: 2.01 (0.68), residues: 40 sheet: 0.17 (0.27), residues: 359 loop : -0.96 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 96 TYR 0.018 0.002 TYR C 91 PHE 0.029 0.003 PHE C 100C TRP 0.022 0.002 TRP H 47 HIS 0.008 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 6685) covalent geometry : angle 0.75860 ( 9044) SS BOND : bond 0.00636 ( 9) SS BOND : angle 2.49903 ( 18) hydrogen bonds : bond 0.03966 ( 256) hydrogen bonds : angle 5.74515 ( 663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.258 Fit side-chains REVERT: A 21 SER cc_start: 0.8072 (m) cc_final: 0.7869 (p) REVERT: C 16 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7022 (ttm110) REVERT: C 39 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.7104 (tt0) REVERT: D 18 ARG cc_start: 0.7190 (mmm160) cc_final: 0.6945 (mmt180) REVERT: L 92 THR cc_start: 0.8910 (t) cc_final: 0.8685 (t) outliers start: 32 outliers final: 25 residues processed: 153 average time/residue: 0.0856 time to fit residues: 17.0651 Evaluate side-chains 155 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 0.0050 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 22 optimal weight: 10.0000 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.214166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.179505 restraints weight = 7917.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.183867 restraints weight = 5345.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.186509 restraints weight = 4069.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.188706 restraints weight = 3391.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.189788 restraints weight = 2968.561| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 1.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6694 Z= 0.135 Angle : 0.669 10.189 9062 Z= 0.350 Chirality : 0.045 0.149 977 Planarity : 0.005 0.060 1152 Dihedral : 5.119 22.776 905 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.37 % Favored : 93.50 % Rotamer: Outliers : 4.03 % Allowed : 21.39 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.30), residues: 816 helix: 2.36 (0.68), residues: 40 sheet: 0.29 (0.27), residues: 355 loop : -1.05 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 19 TYR 0.014 0.001 TYR L 91 PHE 0.026 0.002 PHE C 100C TRP 0.022 0.001 TRP H 47 HIS 0.007 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6685) covalent geometry : angle 0.66518 ( 9044) SS BOND : bond 0.00464 ( 9) SS BOND : angle 1.78592 ( 18) hydrogen bonds : bond 0.03188 ( 256) hydrogen bonds : angle 5.18002 ( 663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1309.84 seconds wall clock time: 23 minutes 16.04 seconds (1396.04 seconds total)