Starting phenix.real_space_refine on Sat May 10 00:23:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxe_37904/05_2025/8wxe_37904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxe_37904/05_2025/8wxe_37904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wxe_37904/05_2025/8wxe_37904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxe_37904/05_2025/8wxe_37904.map" model { file = "/net/cci-nas-00/data/ceres_data/8wxe_37904/05_2025/8wxe_37904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxe_37904/05_2025/8wxe_37904.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.003 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 37 5.16 5 C 2865 2.51 5 N 692 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4388 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 226 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "b" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 226 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 853 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 2 Chain: "f" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 847 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 2 Chain: "g" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 821 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain breaks: 2 Chain: "m" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 268 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "n" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.20, per 1000 atoms: 0.73 Number of scatterers: 4388 At special positions: 0 Unit cell: (94.569, 82.612, 98.917, 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 37 16.00 O 794 8.00 N 692 7.00 C 2865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 473.7 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 42.2% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'a' and resid 27 through 54 removed outlier: 4.323A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP a 36 " --> pdb=" O CYS a 32 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE a 38 " --> pdb=" O LEU a 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 54 Processing helix chain 'd' and resid 100 through 125 removed outlier: 3.787A pdb=" N VAL d 104 " --> pdb=" O ASP d 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR d 110 " --> pdb=" O GLY d 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 152 removed outlier: 3.706A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE e 133 " --> pdb=" O SER e 129 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL e 134 " --> pdb=" O VAL e 130 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE e 135 " --> pdb=" O ALA e 131 " (cutoff:3.500A) Processing helix chain 'f' and resid 128 through 153 Processing helix chain 'g' and resid 111 through 140 removed outlier: 4.749A pdb=" N GLY g 117 " --> pdb=" O ALA g 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 258 through 288 removed outlier: 3.667A pdb=" N PHE m 288 " --> pdb=" O THR m 284 " (cutoff:3.500A) Processing helix chain 'n' and resid 253 through 288 removed outlier: 3.891A pdb=" N TYR n 264 " --> pdb=" O THR n 260 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET n 265 " --> pdb=" O SER n 261 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL n 275 " --> pdb=" O LEU n 271 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR n 276 " --> pdb=" O LYS n 272 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS n 283 " --> pdb=" O ILE n 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 33 through 36 removed outlier: 7.108A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 41 through 46 removed outlier: 3.668A pdb=" N VAL d 44 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY d 69 " --> pdb=" O VAL d 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL d 88 " --> pdb=" O GLY d 69 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR d 71 " --> pdb=" O VAL d 86 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL d 86 " --> pdb=" O TYR d 71 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL e 97 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR e 99 " --> pdb=" O LEU e 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 40 removed outlier: 4.132A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER e 83 " --> pdb=" O GLY e 76 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY e 76 " --> pdb=" O SER e 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 45 through 47 removed outlier: 3.536A pdb=" N LEU f 82 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 122 through 123 removed outlier: 3.588A pdb=" N MET f 123 " --> pdb=" O ILE g 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34 removed outlier: 4.439A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 55 through 57 removed outlier: 7.219A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE g 62 " --> pdb=" O TRP g 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'g' and resid 84 through 85 removed outlier: 4.063A pdb=" N TYR g 85 " --> pdb=" O LEU g 97 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU g 97 " --> pdb=" O TYR g 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 215 hydrogen bonds defined for protein. 624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1333 1.34 - 1.47: 1083 1.47 - 1.59: 2000 1.59 - 1.71: 1 1.71 - 1.83: 51 Bond restraints: 4468 Sorted by residual: bond pdb=" CB PRO g 96 " pdb=" CG PRO g 96 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.72e+00 bond pdb=" C ASP a 28 " pdb=" N PRO a 29 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.10e+00 bond pdb=" N PRO g 96 " pdb=" CA PRO g 96 " ideal model delta sigma weight residual 1.469 1.450 0.018 1.28e-02 6.10e+03 2.05e+00 bond pdb=" CB CYS a 32 " pdb=" SG CYS a 32 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" C3 CLR g 201 " pdb=" O1 CLR g 201 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 4463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 5950 2.74 - 5.48: 76 5.48 - 8.22: 17 8.22 - 10.96: 6 10.96 - 13.70: 2 Bond angle restraints: 6051 Sorted by residual: angle pdb=" CA PRO g 96 " pdb=" N PRO g 96 " pdb=" CD PRO g 96 " ideal model delta sigma weight residual 112.00 98.30 13.70 1.40e+00 5.10e-01 9.58e+01 angle pdb=" CA GLU f 106 " pdb=" CB GLU f 106 " pdb=" CG GLU f 106 " ideal model delta sigma weight residual 114.10 123.42 -9.32 2.00e+00 2.50e-01 2.17e+01 angle pdb=" CB MET f 123 " pdb=" CG MET f 123 " pdb=" SD MET f 123 " ideal model delta sigma weight residual 112.70 124.29 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" N PRO g 96 " pdb=" CD PRO g 96 " pdb=" CG PRO g 96 " ideal model delta sigma weight residual 103.20 97.67 5.53 1.50e+00 4.44e-01 1.36e+01 angle pdb=" N PRO g 96 " pdb=" CA PRO g 96 " pdb=" CB PRO g 96 " ideal model delta sigma weight residual 103.25 99.87 3.38 1.05e+00 9.07e-01 1.04e+01 ... (remaining 6046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 2228 17.86 - 35.72: 372 35.72 - 53.58: 94 53.58 - 71.44: 20 71.44 - 89.30: 4 Dihedral angle restraints: 2718 sinusoidal: 1122 harmonic: 1596 Sorted by residual: dihedral pdb=" CB CYS a 32 " pdb=" SG CYS a 32 " pdb=" SG CYS b 32 " pdb=" CB CYS b 32 " ideal model delta sinusoidal sigma weight residual -86.00 -158.21 72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -147.58 61.58 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS d 37 " pdb=" SG CYS d 37 " pdb=" SG CYS d 73 " pdb=" CB CYS d 73 " ideal model delta sinusoidal sigma weight residual -86.00 -132.94 46.94 1 1.00e+01 1.00e-02 3.05e+01 ... (remaining 2715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 472 0.034 - 0.068: 170 0.068 - 0.102: 53 0.102 - 0.136: 21 0.136 - 0.170: 5 Chirality restraints: 721 Sorted by residual: chirality pdb=" CA PRO f 105 " pdb=" N PRO f 105 " pdb=" C PRO f 105 " pdb=" CB PRO f 105 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" C20 CLR g 201 " pdb=" C17 CLR g 201 " pdb=" C21 CLR g 201 " pdb=" C22 CLR g 201 " both_signs ideal model delta sigma weight residual False 2.59 2.43 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ASN g 28 " pdb=" N ASN g 28 " pdb=" C ASN g 28 " pdb=" CB ASN g 28 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 718 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS g 95 " 0.119 5.00e-02 4.00e+02 1.68e-01 4.53e+01 pdb=" N PRO g 96 " -0.290 5.00e-02 4.00e+02 pdb=" CA PRO g 96 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO g 96 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE d 24 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO d 25 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO d 25 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO d 25 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU f 86 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" CD GLU f 86 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU f 86 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU f 86 " -0.013 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 223 2.72 - 3.27: 4463 3.27 - 3.81: 7031 3.81 - 4.36: 7314 4.36 - 4.90: 12724 Nonbonded interactions: 31755 Sorted by model distance: nonbonded pdb=" O SER f 41 " pdb=" OG1 THR f 44 " model vdw 2.178 3.040 nonbonded pdb=" NZ LYS f 104 " pdb=" OE1 GLU f 106 " model vdw 2.199 3.120 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.216 3.040 nonbonded pdb=" N GLU e 124 " pdb=" OE1 GLU e 124 " model vdw 2.272 3.120 nonbonded pdb=" OG SER g 125 " pdb=" NZ LYS n 272 " model vdw 2.321 3.120 ... (remaining 31750 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 'b' } ncs_group { reference = (chain 'e' and (resid 33 through 49 or resid 58 through 65 or resid 75 through 1 \ 53)) selection = (chain 'f' and (resid 33 through 65 or resid 75 through 101 or resid 109 through \ 153)) } 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.270 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 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 : 0.004 0.130 4477 Z= 0.171 Angle : 0.867 13.704 6069 Z= 0.453 Chirality : 0.043 0.170 721 Planarity : 0.008 0.168 728 Dihedral : 18.180 89.302 1663 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.04 % Allowed : 40.73 % Favored : 57.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.35), residues: 520 helix: 1.55 (0.33), residues: 217 sheet: -1.07 (0.61), residues: 71 loop : -2.43 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP e 59 HIS 0.005 0.001 HIS g 29 PHE 0.009 0.001 PHE f 110 TYR 0.023 0.001 TYR f 36 ARG 0.007 0.001 ARG e 115 Details of bonding type rmsd hydrogen bonds : bond 0.18141 ( 215) hydrogen bonds : angle 6.34218 ( 624) SS BOND : bond 0.00235 ( 9) SS BOND : angle 1.90872 ( 18) covalent geometry : bond 0.00385 ( 4468) covalent geometry : angle 0.86203 ( 6051) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 52 ARG cc_start: 0.6571 (ttt180) cc_final: 0.6177 (ttt180) REVERT: d 63 ARG cc_start: 0.8723 (ttm170) cc_final: 0.8450 (mtp85) REVERT: d 92 MET cc_start: 0.8431 (mtp) cc_final: 0.7769 (mmt) REVERT: d 97 VAL cc_start: 0.8955 (t) cc_final: 0.8619 (p) REVERT: d 109 VAL cc_start: 0.8934 (m) cc_final: 0.8674 (p) REVERT: e 92 GLN cc_start: 0.8518 (tt0) cc_final: 0.8028 (tt0) REVERT: e 95 TYR cc_start: 0.6958 (m-80) cc_final: 0.6366 (m-10) REVERT: e 145 LEU cc_start: 0.8539 (mm) cc_final: 0.8173 (tt) REVERT: e 147 LEU cc_start: 0.8127 (tt) cc_final: 0.7907 (mm) REVERT: f 97 VAL cc_start: 0.8610 (m) cc_final: 0.8233 (p) REVERT: f 101 ARG cc_start: 0.7297 (mmt90) cc_final: 0.7068 (mpt180) REVERT: f 121 ASN cc_start: 0.9297 (t0) cc_final: 0.8889 (t0) REVERT: f 125 MET cc_start: 0.7019 (pmm) cc_final: 0.6524 (pmm) REVERT: g 34 TYR cc_start: 0.8520 (t80) cc_final: 0.8285 (t80) REVERT: g 39 ASP cc_start: 0.7355 (m-30) cc_final: 0.6303 (m-30) REVERT: g 73 ASN cc_start: 0.9503 (t0) cc_final: 0.9215 (t0) REVERT: g 103 MET cc_start: 0.7179 (mmp) cc_final: 0.6798 (mmp) REVERT: g 119 LEU cc_start: 0.9204 (tp) cc_final: 0.8856 (tp) REVERT: n 259 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7496 (t0) outliers start: 10 outliers final: 5 residues processed: 221 average time/residue: 0.1524 time to fit residues: 41.8907 Evaluate side-chains 164 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain n residue 259 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 89 HIS e 92 GLN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.136394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104030 restraints weight = 10017.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.107140 restraints weight = 6780.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.107889 restraints weight = 4513.733| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4477 Z= 0.240 Angle : 0.843 8.244 6069 Z= 0.427 Chirality : 0.046 0.178 721 Planarity : 0.006 0.088 728 Dihedral : 7.927 58.239 662 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 9.98 % Allowed : 33.81 % Favored : 56.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.34), residues: 520 helix: 1.82 (0.32), residues: 224 sheet: -1.24 (0.57), residues: 77 loop : -2.56 (0.34), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP e 59 HIS 0.003 0.001 HIS g 29 PHE 0.024 0.002 PHE g 127 TYR 0.027 0.002 TYR f 149 ARG 0.005 0.001 ARG g 82 Details of bonding type rmsd hydrogen bonds : bond 0.05199 ( 215) hydrogen bonds : angle 4.75411 ( 624) SS BOND : bond 0.00630 ( 9) SS BOND : angle 2.22724 ( 18) covalent geometry : bond 0.00552 ( 4468) covalent geometry : angle 0.83527 ( 6051) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 46 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7398 (tt) REVERT: a 52 ARG cc_start: 0.6590 (ttt180) cc_final: 0.6212 (ttt180) REVERT: b 34 LEU cc_start: 0.8032 (tt) cc_final: 0.7339 (mm) REVERT: d 63 ARG cc_start: 0.8986 (ttm170) cc_final: 0.8290 (mtp-110) REVERT: d 72 ARG cc_start: 0.7883 (tpt-90) cc_final: 0.7414 (tpt-90) REVERT: d 92 MET cc_start: 0.8148 (mtp) cc_final: 0.7658 (mmt) REVERT: d 97 VAL cc_start: 0.8828 (t) cc_final: 0.8604 (p) REVERT: d 98 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7317 (tm-30) REVERT: d 120 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8458 (tp) REVERT: e 92 GLN cc_start: 0.8631 (tt0) cc_final: 0.8283 (tt0) REVERT: e 145 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8086 (tt) REVERT: e 147 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8027 (mm) REVERT: f 121 ASN cc_start: 0.9219 (t0) cc_final: 0.8731 (t0) REVERT: f 125 MET cc_start: 0.7457 (pmm) cc_final: 0.7218 (pmm) REVERT: g 34 TYR cc_start: 0.8777 (t80) cc_final: 0.8472 (t80) REVERT: g 38 GLU cc_start: 0.8102 (pm20) cc_final: 0.7559 (pm20) REVERT: g 73 ASN cc_start: 0.9469 (t0) cc_final: 0.9241 (t0) REVERT: g 82 ARG cc_start: 0.8907 (mmt90) cc_final: 0.8544 (mmt-90) REVERT: g 111 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8610 (p0) REVERT: g 119 LEU cc_start: 0.9104 (tp) cc_final: 0.8804 (tp) REVERT: m 261 MET cc_start: 0.8533 (mmm) cc_final: 0.8280 (tpp) REVERT: n 259 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7240 (t0) REVERT: n 271 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7782 (tm) outliers start: 49 outliers final: 28 residues processed: 197 average time/residue: 0.1454 time to fit residues: 36.0721 Evaluate side-chains 191 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 56 PHE Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 276 THR Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 271 LEU Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 61 HIS m 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.139899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.107967 restraints weight = 9799.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.111304 restraints weight = 6668.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.112261 restraints weight = 4309.668| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4477 Z= 0.142 Angle : 0.731 8.176 6069 Z= 0.366 Chirality : 0.042 0.154 721 Planarity : 0.004 0.061 728 Dihedral : 7.509 58.355 658 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 9.37 % Allowed : 36.86 % Favored : 53.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.35), residues: 520 helix: 2.31 (0.32), residues: 221 sheet: -0.98 (0.61), residues: 71 loop : -2.60 (0.32), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 59 HIS 0.002 0.001 HIS e 61 PHE 0.023 0.002 PHE g 120 TYR 0.014 0.001 TYR e 111 ARG 0.007 0.001 ARG b 52 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 215) hydrogen bonds : angle 4.18235 ( 624) SS BOND : bond 0.00437 ( 9) SS BOND : angle 1.74081 ( 18) covalent geometry : bond 0.00312 ( 4468) covalent geometry : angle 0.72567 ( 6051) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 46 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7265 (tt) REVERT: a 52 ARG cc_start: 0.6548 (ttt180) cc_final: 0.6091 (ttt180) REVERT: b 34 LEU cc_start: 0.7964 (tt) cc_final: 0.7274 (mm) REVERT: b 52 ARG cc_start: 0.7336 (ttp80) cc_final: 0.7051 (tpp80) REVERT: d 63 ARG cc_start: 0.8999 (ttm170) cc_final: 0.8334 (mtp-110) REVERT: d 72 ARG cc_start: 0.7806 (tpt-90) cc_final: 0.7580 (tpt-90) REVERT: d 92 MET cc_start: 0.8127 (mtp) cc_final: 0.7560 (mmt) REVERT: d 98 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7855 (tm-30) REVERT: d 120 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8344 (tp) REVERT: e 92 GLN cc_start: 0.8592 (tt0) cc_final: 0.8137 (tt0) REVERT: e 122 CYS cc_start: 0.6286 (t) cc_final: 0.6023 (t) REVERT: e 145 LEU cc_start: 0.8581 (mm) cc_final: 0.8092 (tt) REVERT: e 147 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7893 (mm) REVERT: f 104 LYS cc_start: 0.9265 (ttmt) cc_final: 0.8933 (ptmm) REVERT: f 120 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8656 (tm-30) REVERT: f 121 ASN cc_start: 0.9217 (t0) cc_final: 0.8673 (t0) REVERT: f 125 MET cc_start: 0.7321 (pmm) cc_final: 0.7075 (pmm) REVERT: g 34 TYR cc_start: 0.8801 (t80) cc_final: 0.8512 (t80) REVERT: g 61 MET cc_start: 0.6539 (tpt) cc_final: 0.5683 (mmm) REVERT: g 73 ASN cc_start: 0.9466 (t0) cc_final: 0.9197 (t0) REVERT: g 82 ARG cc_start: 0.8606 (mmt90) cc_final: 0.8321 (mmt-90) REVERT: g 119 LEU cc_start: 0.9013 (tp) cc_final: 0.8740 (tp) REVERT: n 259 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7117 (t0) outliers start: 46 outliers final: 22 residues processed: 192 average time/residue: 0.1468 time to fit residues: 35.3212 Evaluate side-chains 177 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.0670 chunk 23 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 chunk 5 optimal weight: 6.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.140034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108131 restraints weight = 9869.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.111264 restraints weight = 6848.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.112164 restraints weight = 4483.749| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4477 Z= 0.139 Angle : 0.742 9.658 6069 Z= 0.363 Chirality : 0.042 0.190 721 Planarity : 0.004 0.048 728 Dihedral : 7.189 54.699 658 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 9.16 % Allowed : 37.88 % Favored : 52.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.35), residues: 520 helix: 2.21 (0.32), residues: 221 sheet: -0.99 (0.60), residues: 71 loop : -2.58 (0.32), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP e 59 HIS 0.002 0.001 HIS e 61 PHE 0.030 0.002 PHE a 40 TYR 0.020 0.001 TYR g 100 ARG 0.004 0.000 ARG b 52 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 215) hydrogen bonds : angle 3.95494 ( 624) SS BOND : bond 0.00258 ( 9) SS BOND : angle 1.68129 ( 18) covalent geometry : bond 0.00311 ( 4468) covalent geometry : angle 0.73756 ( 6051) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 46 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7246 (tt) REVERT: a 52 ARG cc_start: 0.6513 (ttt180) cc_final: 0.5995 (ttt180) REVERT: b 34 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7099 (mm) REVERT: d 63 ARG cc_start: 0.8920 (ttm170) cc_final: 0.8242 (mtp-110) REVERT: d 72 ARG cc_start: 0.7888 (tpt-90) cc_final: 0.7614 (tpt-90) REVERT: d 92 MET cc_start: 0.8182 (mtp) cc_final: 0.7611 (mmt) REVERT: d 98 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7556 (tm-30) REVERT: d 120 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8241 (tp) REVERT: e 92 GLN cc_start: 0.8487 (tt0) cc_final: 0.8025 (tt0) REVERT: e 115 ARG cc_start: 0.8487 (ttm110) cc_final: 0.8231 (ttm110) REVERT: e 145 LEU cc_start: 0.8556 (mm) cc_final: 0.8083 (tt) REVERT: e 147 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7922 (mm) REVERT: f 61 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.6469 (t70) REVERT: f 104 LYS cc_start: 0.9331 (ttmt) cc_final: 0.8739 (ttpp) REVERT: f 106 GLU cc_start: 0.7974 (mp0) cc_final: 0.7697 (mp0) REVERT: f 120 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8540 (tm-30) REVERT: f 121 ASN cc_start: 0.9166 (t0) cc_final: 0.8570 (t0) REVERT: f 125 MET cc_start: 0.7295 (pmm) cc_final: 0.7020 (pmm) REVERT: g 34 TYR cc_start: 0.8882 (t80) cc_final: 0.8557 (t80) REVERT: g 38 GLU cc_start: 0.8175 (pm20) cc_final: 0.7764 (pm20) REVERT: g 61 MET cc_start: 0.6570 (tpt) cc_final: 0.5707 (mmm) REVERT: g 73 ASN cc_start: 0.9454 (t0) cc_final: 0.9241 (t0) REVERT: g 119 LEU cc_start: 0.9050 (tp) cc_final: 0.8750 (tp) REVERT: m 261 MET cc_start: 0.8489 (mmm) cc_final: 0.8174 (tpt) REVERT: n 259 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7027 (t0) outliers start: 45 outliers final: 27 residues processed: 184 average time/residue: 0.1556 time to fit residues: 35.5729 Evaluate side-chains 187 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.135883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.103685 restraints weight = 10146.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106890 restraints weight = 6989.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.107712 restraints weight = 4646.058| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4477 Z= 0.173 Angle : 0.749 10.499 6069 Z= 0.372 Chirality : 0.043 0.165 721 Planarity : 0.004 0.038 728 Dihedral : 7.016 53.637 657 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 9.98 % Allowed : 36.46 % Favored : 53.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.35), residues: 520 helix: 2.04 (0.32), residues: 225 sheet: -0.94 (0.57), residues: 83 loop : -2.75 (0.31), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP e 59 HIS 0.002 0.001 HIS d 89 PHE 0.027 0.002 PHE g 120 TYR 0.018 0.002 TYR f 149 ARG 0.004 0.001 ARG g 82 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 215) hydrogen bonds : angle 4.08774 ( 624) SS BOND : bond 0.00287 ( 9) SS BOND : angle 2.13109 ( 18) covalent geometry : bond 0.00396 ( 4468) covalent geometry : angle 0.74077 ( 6051) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.5383 (t80) REVERT: a 46 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7326 (tt) REVERT: a 52 ARG cc_start: 0.6717 (ttt180) cc_final: 0.6079 (ttt180) REVERT: b 34 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7301 (mm) REVERT: b 40 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.7972 (t80) REVERT: d 63 ARG cc_start: 0.8999 (ttm170) cc_final: 0.8266 (mtp-110) REVERT: d 72 ARG cc_start: 0.7990 (tpt-90) cc_final: 0.7707 (tpt-90) REVERT: d 92 MET cc_start: 0.8255 (mtp) cc_final: 0.7763 (mmt) REVERT: d 98 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7314 (tp30) REVERT: e 87 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8052 (t80) REVERT: e 115 ARG cc_start: 0.8488 (ttm110) cc_final: 0.7841 (ttm110) REVERT: e 120 GLU cc_start: 0.7285 (tm-30) cc_final: 0.7054 (tm-30) REVERT: e 145 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8227 (tt) REVERT: e 147 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7838 (mm) REVERT: f 59 TRP cc_start: 0.7809 (m100) cc_final: 0.7103 (m100) REVERT: f 61 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6503 (t-90) REVERT: f 104 LYS cc_start: 0.9410 (ttmt) cc_final: 0.8932 (ttpt) REVERT: f 121 ASN cc_start: 0.9123 (t0) cc_final: 0.8477 (t0) REVERT: f 125 MET cc_start: 0.7436 (pmm) cc_final: 0.7089 (pmm) REVERT: g 34 TYR cc_start: 0.8865 (t80) cc_final: 0.8478 (t80) REVERT: g 73 ASN cc_start: 0.9447 (t0) cc_final: 0.9244 (t0) REVERT: g 119 LEU cc_start: 0.9055 (tp) cc_final: 0.8761 (tp) REVERT: g 129 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8289 (mt) REVERT: m 261 MET cc_start: 0.8633 (mmm) cc_final: 0.8342 (tpt) REVERT: m 272 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7923 (mp) REVERT: n 259 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7345 (t0) outliers start: 49 outliers final: 33 residues processed: 189 average time/residue: 0.1519 time to fit residues: 36.0508 Evaluate side-chains 199 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 272 LEU Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.138234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.107133 restraints weight = 9910.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.109400 restraints weight = 7516.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.110081 restraints weight = 5051.721| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4477 Z= 0.138 Angle : 0.754 10.931 6069 Z= 0.369 Chirality : 0.042 0.155 721 Planarity : 0.004 0.032 728 Dihedral : 6.863 54.791 655 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 8.96 % Allowed : 36.66 % Favored : 54.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.35), residues: 520 helix: 2.14 (0.33), residues: 222 sheet: -0.89 (0.57), residues: 83 loop : -2.64 (0.32), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP e 59 HIS 0.001 0.001 HIS e 61 PHE 0.034 0.002 PHE e 110 TYR 0.012 0.001 TYR e 36 ARG 0.002 0.000 ARG b 52 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 215) hydrogen bonds : angle 3.84082 ( 624) SS BOND : bond 0.00301 ( 9) SS BOND : angle 1.71461 ( 18) covalent geometry : bond 0.00310 ( 4468) covalent geometry : angle 0.74935 ( 6051) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.4978 (t80) REVERT: a 46 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7249 (tt) REVERT: a 52 ARG cc_start: 0.6588 (ttt180) cc_final: 0.5943 (ttt180) REVERT: b 34 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7207 (mm) REVERT: b 40 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7701 (t80) REVERT: d 59 ASP cc_start: 0.7776 (p0) cc_final: 0.6790 (t0) REVERT: d 63 ARG cc_start: 0.8984 (ttm170) cc_final: 0.8237 (mtp-110) REVERT: d 92 MET cc_start: 0.8302 (mtp) cc_final: 0.7770 (mmt) REVERT: d 98 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7371 (tm-30) REVERT: e 115 ARG cc_start: 0.8490 (ttm110) cc_final: 0.7833 (ttm110) REVERT: e 145 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8165 (tt) REVERT: e 147 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7873 (mm) REVERT: f 61 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6868 (t-90) REVERT: f 104 LYS cc_start: 0.9385 (ttmt) cc_final: 0.8971 (ttpp) REVERT: f 106 GLU cc_start: 0.7983 (mp0) cc_final: 0.7718 (mp0) REVERT: f 110 PHE cc_start: 0.7220 (p90) cc_final: 0.6919 (p90) REVERT: f 120 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8516 (tm-30) REVERT: f 121 ASN cc_start: 0.9116 (t0) cc_final: 0.8475 (t0) REVERT: f 125 MET cc_start: 0.7251 (pmm) cc_final: 0.6886 (pmm) REVERT: g 73 ASN cc_start: 0.9459 (t0) cc_final: 0.9244 (t0) REVERT: g 82 ARG cc_start: 0.8646 (mmt90) cc_final: 0.8225 (mmt-90) REVERT: g 100 TYR cc_start: 0.7699 (t80) cc_final: 0.7451 (t80) REVERT: g 119 LEU cc_start: 0.9062 (tp) cc_final: 0.8772 (tp) REVERT: m 258 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8137 (mmmm) REVERT: m 261 MET cc_start: 0.8592 (mmm) cc_final: 0.8232 (tpt) REVERT: m 286 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8050 (tptp) REVERT: n 259 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7060 (t0) outliers start: 44 outliers final: 26 residues processed: 178 average time/residue: 0.1621 time to fit residues: 35.8573 Evaluate side-chains 182 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 46 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.136885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105953 restraints weight = 9941.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.108125 restraints weight = 7372.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.108907 restraints weight = 4984.520| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4477 Z= 0.151 Angle : 0.765 10.718 6069 Z= 0.377 Chirality : 0.042 0.150 721 Planarity : 0.003 0.025 728 Dihedral : 6.642 52.287 655 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 9.78 % Allowed : 38.29 % Favored : 51.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.35), residues: 520 helix: 2.09 (0.32), residues: 222 sheet: -0.94 (0.57), residues: 83 loop : -2.66 (0.32), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP e 59 HIS 0.001 0.000 HIS e 61 PHE 0.026 0.002 PHE g 120 TYR 0.017 0.001 TYR e 36 ARG 0.003 0.000 ARG g 82 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 215) hydrogen bonds : angle 3.83695 ( 624) SS BOND : bond 0.00429 ( 9) SS BOND : angle 2.09781 ( 18) covalent geometry : bond 0.00345 ( 4468) covalent geometry : angle 0.75709 ( 6051) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.5905 (t80) REVERT: a 52 ARG cc_start: 0.6634 (ttt180) cc_final: 0.5922 (ttt180) REVERT: b 34 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7256 (mm) REVERT: b 40 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7829 (t80) REVERT: d 59 ASP cc_start: 0.7731 (p0) cc_final: 0.6746 (t0) REVERT: d 63 ARG cc_start: 0.8996 (ttm170) cc_final: 0.8286 (mtp-110) REVERT: d 72 ARG cc_start: 0.7899 (tpt-90) cc_final: 0.7654 (tpp-160) REVERT: d 92 MET cc_start: 0.8314 (mtp) cc_final: 0.7788 (mmt) REVERT: d 98 GLU cc_start: 0.8130 (tm-30) cc_final: 0.6630 (tm-30) REVERT: e 87 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.8242 (t80) REVERT: e 115 ARG cc_start: 0.8491 (ttm110) cc_final: 0.8182 (ttm110) REVERT: e 145 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8217 (tt) REVERT: e 147 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7833 (mm) REVERT: f 61 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6844 (t-90) REVERT: f 104 LYS cc_start: 0.9390 (ttmt) cc_final: 0.9018 (ttpt) REVERT: f 110 PHE cc_start: 0.7325 (p90) cc_final: 0.7009 (p90) REVERT: f 120 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8594 (tm-30) REVERT: f 121 ASN cc_start: 0.9097 (t0) cc_final: 0.8402 (t0) REVERT: f 125 MET cc_start: 0.7261 (pmm) cc_final: 0.6915 (pmm) REVERT: g 34 TYR cc_start: 0.8707 (t80) cc_final: 0.8291 (t80) REVERT: g 73 ASN cc_start: 0.9497 (t0) cc_final: 0.9239 (t0) REVERT: g 74 LEU cc_start: 0.8786 (tt) cc_final: 0.8347 (mt) REVERT: g 119 LEU cc_start: 0.9055 (tp) cc_final: 0.8766 (tp) REVERT: g 129 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8148 (mt) REVERT: m 258 LYS cc_start: 0.8816 (mmmm) cc_final: 0.8213 (mmmm) REVERT: m 261 MET cc_start: 0.8625 (mmm) cc_final: 0.8229 (tpt) REVERT: m 286 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8097 (tptp) REVERT: n 259 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7141 (t0) outliers start: 48 outliers final: 32 residues processed: 181 average time/residue: 0.1506 time to fit residues: 34.1759 Evaluate side-chains 193 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.136414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.105476 restraints weight = 9893.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.107573 restraints weight = 7383.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108345 restraints weight = 4989.942| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4477 Z= 0.152 Angle : 0.787 10.315 6069 Z= 0.387 Chirality : 0.042 0.151 721 Planarity : 0.003 0.023 728 Dihedral : 6.712 51.486 655 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 9.98 % Allowed : 37.88 % Favored : 52.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.35), residues: 520 helix: 2.09 (0.32), residues: 222 sheet: -0.88 (0.57), residues: 83 loop : -2.65 (0.32), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP e 59 HIS 0.002 0.001 HIS e 61 PHE 0.035 0.002 PHE a 40 TYR 0.028 0.002 TYR d 79 ARG 0.003 0.000 ARG g 82 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 215) hydrogen bonds : angle 3.77637 ( 624) SS BOND : bond 0.00385 ( 9) SS BOND : angle 2.27144 ( 18) covalent geometry : bond 0.00352 ( 4468) covalent geometry : angle 0.77834 ( 6051) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6373 (t80) REVERT: a 52 ARG cc_start: 0.6648 (ttt180) cc_final: 0.5959 (ttt180) REVERT: b 34 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7295 (mm) REVERT: b 40 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7812 (t80) REVERT: d 63 ARG cc_start: 0.9012 (ttm170) cc_final: 0.8297 (mtp-110) REVERT: d 72 ARG cc_start: 0.7852 (tpt-90) cc_final: 0.7441 (tpp-160) REVERT: d 92 MET cc_start: 0.8302 (mtp) cc_final: 0.7816 (mmt) REVERT: d 98 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7234 (tm-30) REVERT: e 87 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8230 (t80) REVERT: e 115 ARG cc_start: 0.8502 (ttm110) cc_final: 0.8236 (ttm110) REVERT: e 145 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8199 (tt) REVERT: e 147 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7838 (mm) REVERT: f 61 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6888 (t-90) REVERT: f 104 LYS cc_start: 0.9385 (ttmt) cc_final: 0.9019 (ttpp) REVERT: f 110 PHE cc_start: 0.7446 (p90) cc_final: 0.7125 (p90) REVERT: f 120 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8592 (tm-30) REVERT: f 121 ASN cc_start: 0.9091 (t0) cc_final: 0.8304 (t0) REVERT: f 125 MET cc_start: 0.7214 (pmm) cc_final: 0.6868 (pmm) REVERT: g 73 ASN cc_start: 0.9470 (t0) cc_final: 0.9264 (t0) REVERT: g 119 LEU cc_start: 0.9051 (tp) cc_final: 0.8738 (tp) REVERT: m 258 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8132 (mmmm) REVERT: m 261 MET cc_start: 0.8649 (mmm) cc_final: 0.8311 (tpt) REVERT: m 286 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8097 (tptp) REVERT: n 256 GLN cc_start: 0.7655 (tm-30) cc_final: 0.7258 (tm-30) REVERT: n 259 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7116 (t0) outliers start: 49 outliers final: 37 residues processed: 176 average time/residue: 0.1595 time to fit residues: 35.1249 Evaluate side-chains 198 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.138234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.106450 restraints weight = 9896.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.110076 restraints weight = 6605.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.111125 restraints weight = 4067.153| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4477 Z= 0.142 Angle : 0.800 9.570 6069 Z= 0.394 Chirality : 0.042 0.151 721 Planarity : 0.003 0.025 728 Dihedral : 6.728 52.221 655 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.96 % Allowed : 38.90 % Favored : 52.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.35), residues: 520 helix: 2.16 (0.33), residues: 222 sheet: -0.97 (0.60), residues: 71 loop : -2.55 (0.32), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP e 59 HIS 0.002 0.001 HIS e 61 PHE 0.025 0.002 PHE g 120 TYR 0.022 0.002 TYR n 276 ARG 0.002 0.000 ARG g 82 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 215) hydrogen bonds : angle 3.71562 ( 624) SS BOND : bond 0.00284 ( 9) SS BOND : angle 2.41493 ( 18) covalent geometry : bond 0.00326 ( 4468) covalent geometry : angle 0.79078 ( 6051) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.5984 (t80) REVERT: a 52 ARG cc_start: 0.6704 (ttt180) cc_final: 0.5955 (ttt180) REVERT: b 34 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7220 (mm) REVERT: b 40 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7562 (t80) REVERT: d 63 ARG cc_start: 0.8996 (ttm170) cc_final: 0.8244 (mtp-110) REVERT: d 72 ARG cc_start: 0.7843 (tpt-90) cc_final: 0.7453 (tpp-160) REVERT: d 92 MET cc_start: 0.8291 (mtp) cc_final: 0.7804 (mmt) REVERT: d 98 GLU cc_start: 0.8108 (tm-30) cc_final: 0.6736 (tm-30) REVERT: e 87 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8198 (t80) REVERT: e 115 ARG cc_start: 0.8496 (ttm110) cc_final: 0.8195 (ttm110) REVERT: e 125 MET cc_start: 0.8295 (ptp) cc_final: 0.7780 (ptt) REVERT: e 145 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8193 (tt) REVERT: e 147 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7923 (mm) REVERT: f 104 LYS cc_start: 0.9336 (ttmt) cc_final: 0.8994 (ttpp) REVERT: f 110 PHE cc_start: 0.7523 (p90) cc_final: 0.7207 (p90) REVERT: f 121 ASN cc_start: 0.9112 (t0) cc_final: 0.8375 (t0) REVERT: f 125 MET cc_start: 0.7147 (pmm) cc_final: 0.6780 (pmm) REVERT: f 146 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8026 (mm) REVERT: g 73 ASN cc_start: 0.9483 (t0) cc_final: 0.9231 (t0) REVERT: g 74 LEU cc_start: 0.8884 (tt) cc_final: 0.8406 (mt) REVERT: g 119 LEU cc_start: 0.9041 (tp) cc_final: 0.8772 (tp) REVERT: m 258 LYS cc_start: 0.8824 (mmmm) cc_final: 0.8176 (mmmm) REVERT: m 261 MET cc_start: 0.8611 (mmm) cc_final: 0.8304 (tpt) REVERT: m 286 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7900 (tptp) REVERT: n 256 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7321 (tm-30) REVERT: n 259 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.6914 (t0) outliers start: 44 outliers final: 31 residues processed: 175 average time/residue: 0.1546 time to fit residues: 33.6500 Evaluate side-chains 185 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 45 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 0.0170 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.139405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.108958 restraints weight = 9730.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.111430 restraints weight = 6923.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.112130 restraints weight = 4605.913| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4477 Z= 0.146 Angle : 0.819 9.448 6069 Z= 0.400 Chirality : 0.043 0.188 721 Planarity : 0.003 0.027 728 Dihedral : 6.674 51.722 655 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 7.94 % Allowed : 39.51 % Favored : 52.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.35), residues: 520 helix: 2.18 (0.33), residues: 222 sheet: -0.98 (0.62), residues: 71 loop : -2.48 (0.32), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP e 59 HIS 0.002 0.001 HIS e 61 PHE 0.031 0.002 PHE a 40 TYR 0.020 0.001 TYR n 276 ARG 0.002 0.000 ARG f 115 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 215) hydrogen bonds : angle 3.69021 ( 624) SS BOND : bond 0.00349 ( 9) SS BOND : angle 2.19695 ( 18) covalent geometry : bond 0.00336 ( 4468) covalent geometry : angle 0.81107 ( 6051) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.4946 (t80) REVERT: a 52 ARG cc_start: 0.6655 (ttt180) cc_final: 0.5943 (ttt180) REVERT: b 34 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7184 (mm) REVERT: b 40 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7874 (t80) REVERT: d 63 ARG cc_start: 0.8989 (ttm170) cc_final: 0.8239 (mtp-110) REVERT: d 72 ARG cc_start: 0.7855 (tpt-90) cc_final: 0.7523 (tpp-160) REVERT: d 92 MET cc_start: 0.8252 (mtp) cc_final: 0.7742 (mmt) REVERT: e 82 LEU cc_start: 0.7959 (mt) cc_final: 0.7713 (mp) REVERT: e 87 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8250 (t80) REVERT: e 115 ARG cc_start: 0.8482 (ttm110) cc_final: 0.8188 (ttm110) REVERT: e 125 MET cc_start: 0.8200 (ptp) cc_final: 0.7726 (ptt) REVERT: e 145 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8185 (tt) REVERT: e 147 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7968 (mm) REVERT: f 104 LYS cc_start: 0.9329 (ttmt) cc_final: 0.8961 (ttpp) REVERT: f 110 PHE cc_start: 0.7550 (p90) cc_final: 0.7245 (p90) REVERT: f 121 ASN cc_start: 0.9154 (t0) cc_final: 0.8093 (t0) REVERT: f 125 MET cc_start: 0.7087 (pmm) cc_final: 0.6718 (pmm) REVERT: f 146 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8089 (mm) REVERT: g 73 ASN cc_start: 0.9516 (t0) cc_final: 0.9263 (t0) REVERT: g 74 LEU cc_start: 0.8784 (tt) cc_final: 0.8330 (mt) REVERT: g 119 LEU cc_start: 0.9032 (tp) cc_final: 0.8775 (tp) REVERT: m 258 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8527 (mmtm) REVERT: m 261 MET cc_start: 0.8535 (mmm) cc_final: 0.8149 (tpt) REVERT: m 286 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7781 (tptp) REVERT: n 256 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7267 (tm-30) REVERT: n 259 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.6873 (t0) outliers start: 39 outliers final: 28 residues processed: 170 average time/residue: 0.1628 time to fit residues: 34.3867 Evaluate side-chains 185 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.133510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.101816 restraints weight = 9809.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.105069 restraints weight = 6845.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.105962 restraints weight = 4392.650| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4477 Z= 0.213 Angle : 0.896 8.462 6069 Z= 0.444 Chirality : 0.047 0.291 721 Planarity : 0.004 0.030 728 Dihedral : 6.703 49.195 655 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.55 % Allowed : 39.71 % Favored : 51.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.35), residues: 520 helix: 1.91 (0.32), residues: 225 sheet: -0.95 (0.59), residues: 83 loop : -2.65 (0.32), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP e 59 HIS 0.003 0.001 HIS d 89 PHE 0.027 0.002 PHE g 120 TYR 0.021 0.002 TYR f 149 ARG 0.007 0.001 ARG g 82 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 215) hydrogen bonds : angle 4.01887 ( 624) SS BOND : bond 0.00470 ( 9) SS BOND : angle 2.66245 ( 18) covalent geometry : bond 0.00500 ( 4468) covalent geometry : angle 0.88565 ( 6051) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1777.52 seconds wall clock time: 31 minutes 45.14 seconds (1905.14 seconds total)