Starting phenix.real_space_refine on Mon Jan 13 22:42:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxe_37904/01_2025/8wxe_37904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxe_37904/01_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_37904/01_2025/8wxe_37904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxe_37904/01_2025/8wxe_37904.map" model { file = "/net/cci-nas-00/data/ceres_data/8wxe_37904/01_2025/8wxe_37904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxe_37904/01_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-5571/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: 3.17, per 1000 atoms: 0.72 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: 1.04 Conformation dependent library (CDL) restraints added in 477.8 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: 0.42 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: 1.05 Time building geometry restraints manager: 1.20 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.840 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.410 ------------------------------------------------------------------------------- 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 4468 Z= 0.244 Angle : 0.862 13.704 6051 Z= 0.451 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 *********************** 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 : 0.476 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: 0.1542 time to fit residues: 42.4030 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 : 0.505 ------------------------------------------------------------------------------- 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: 0.7980 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.136885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104564 restraints weight = 10093.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.107746 restraints weight = 6853.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.108516 restraints weight = 4559.674| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4468 Z= 0.360 Angle : 0.834 8.261 6051 Z= 0.424 Chirality : 0.046 0.159 721 Planarity : 0.005 0.083 728 Dihedral : 7.864 58.159 662 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 9.78 % Allowed : 33.40 % Favored : 56.82 % 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: -0.57 (0.35), residues: 520 helix: 1.83 (0.32), residues: 224 sheet: -1.21 (0.57), residues: 77 loop : -2.55 (0.34), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP g 72 HIS 0.004 0.001 HIS g 29 PHE 0.022 0.002 PHE g 127 TYR 0.026 0.002 TYR f 149 ARG 0.005 0.001 ARG g 82 *********************** 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 216 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 30 LYS cc_start: 0.8469 (tmmt) cc_final: 0.7953 (mmtm) REVERT: a 46 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7388 (tt) REVERT: a 52 ARG cc_start: 0.6552 (ttt180) cc_final: 0.6170 (ttt180) REVERT: b 34 LEU cc_start: 0.7987 (tt) cc_final: 0.7294 (mm) REVERT: d 63 ARG cc_start: 0.8982 (ttm170) cc_final: 0.8253 (mtp-110) REVERT: d 72 ARG cc_start: 0.7802 (tpt-90) cc_final: 0.7315 (tpt-90) REVERT: d 92 MET cc_start: 0.8139 (mtp) cc_final: 0.7610 (mmt) REVERT: d 97 VAL cc_start: 0.8825 (t) cc_final: 0.8604 (p) REVERT: d 98 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7371 (tm-30) REVERT: d 120 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8461 (tp) REVERT: e 92 GLN cc_start: 0.8633 (tt0) cc_final: 0.8287 (tt0) REVERT: e 145 LEU cc_start: 0.8620 (mm) cc_final: 0.8078 (tt) REVERT: e 147 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8024 (mm) REVERT: f 121 ASN cc_start: 0.9213 (t0) cc_final: 0.8738 (t0) REVERT: f 125 MET cc_start: 0.7289 (pmm) cc_final: 0.7072 (pmm) REVERT: g 34 TYR cc_start: 0.8775 (t80) cc_final: 0.8464 (t80) REVERT: g 38 GLU cc_start: 0.8095 (pm20) cc_final: 0.7536 (pm20) REVERT: g 73 ASN cc_start: 0.9476 (t0) cc_final: 0.9239 (t0) REVERT: g 82 ARG cc_start: 0.8887 (mmt90) cc_final: 0.8479 (mmt-90) REVERT: g 111 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8621 (p0) REVERT: g 119 LEU cc_start: 0.9103 (tp) cc_final: 0.8805 (tp) REVERT: m 261 MET cc_start: 0.8541 (mmm) cc_final: 0.8299 (tpp) REVERT: n 259 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7231 (t0) outliers start: 48 outliers final: 28 residues processed: 196 average time/residue: 0.1634 time to fit residues: 40.3878 Evaluate side-chains 189 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.139643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107939 restraints weight = 9844.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.111263 restraints weight = 6637.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.112190 restraints weight = 4195.347| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4468 Z= 0.202 Angle : 0.739 9.031 6051 Z= 0.368 Chirality : 0.042 0.153 721 Planarity : 0.004 0.060 728 Dihedral : 7.499 58.352 658 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 9.98 % Allowed : 36.66 % Favored : 53.36 % 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: -0.29 (0.35), residues: 520 helix: 2.26 (0.32), residues: 221 sheet: -0.96 (0.61), residues: 71 loop : -2.59 (0.32), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP e 59 HIS 0.001 0.001 HIS f 61 PHE 0.024 0.002 PHE e 110 TYR 0.020 0.002 TYR g 100 ARG 0.007 0.001 ARG b 52 *********************** 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 216 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 46 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7263 (tt) REVERT: a 52 ARG cc_start: 0.6583 (ttt180) cc_final: 0.6104 (ttt180) REVERT: b 34 LEU cc_start: 0.7955 (tt) cc_final: 0.7267 (mm) REVERT: d 63 ARG cc_start: 0.8991 (ttm170) cc_final: 0.8310 (mtp-110) REVERT: d 72 ARG cc_start: 0.7784 (tpt-90) cc_final: 0.7444 (tpt-90) REVERT: d 92 MET cc_start: 0.8114 (mtp) cc_final: 0.7558 (mmt) REVERT: d 98 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7836 (tm-30) REVERT: d 120 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8330 (tp) REVERT: e 92 GLN cc_start: 0.8604 (tt0) cc_final: 0.8133 (tt0) REVERT: e 122 CYS cc_start: 0.6397 (t) cc_final: 0.6112 (t) REVERT: e 145 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8122 (tt) REVERT: e 147 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7942 (mm) REVERT: f 61 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.7076 (t70) REVERT: f 104 LYS cc_start: 0.9256 (ttmt) cc_final: 0.8919 (ptmm) REVERT: f 121 ASN cc_start: 0.9203 (t0) cc_final: 0.8680 (t0) REVERT: f 125 MET cc_start: 0.7333 (pmm) cc_final: 0.7074 (pmm) REVERT: g 61 MET cc_start: 0.6654 (tpt) cc_final: 0.5499 (mmm) REVERT: g 73 ASN cc_start: 0.9467 (t0) cc_final: 0.9193 (t0) REVERT: g 119 LEU cc_start: 0.9064 (tp) cc_final: 0.8801 (tp) REVERT: n 259 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7105 (t0) outliers start: 49 outliers final: 25 residues processed: 194 average time/residue: 0.1519 time to fit residues: 37.1301 Evaluate side-chains 186 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 b residue 53 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 145 LEU Chi-restraints excluded: chain e residue 147 LEU 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 137 ASP Chi-restraints excluded: chain f residue 138 ILE 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 61 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.139529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.107686 restraints weight = 9970.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.110920 restraints weight = 6870.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.111508 restraints weight = 4812.053| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4468 Z= 0.189 Angle : 0.733 9.973 6051 Z= 0.362 Chirality : 0.042 0.166 721 Planarity : 0.004 0.045 728 Dihedral : 7.312 55.802 658 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 9.37 % Allowed : 36.05 % Favored : 54.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.30 (0.35), residues: 520 helix: 2.30 (0.32), residues: 219 sheet: -0.84 (0.62), residues: 71 loop : -2.67 (0.30), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 59 HIS 0.008 0.001 HIS f 61 PHE 0.040 0.002 PHE e 110 TYR 0.017 0.002 TYR e 36 ARG 0.003 0.000 ARG b 52 *********************** 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 206 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 46 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7222 (tt) REVERT: a 52 ARG cc_start: 0.6626 (ttt180) cc_final: 0.6108 (ttt180) REVERT: b 34 LEU cc_start: 0.7805 (tt) cc_final: 0.7180 (mm) REVERT: d 63 ARG cc_start: 0.8916 (ttm170) cc_final: 0.8249 (mtp-110) REVERT: d 72 ARG cc_start: 0.7872 (tpt-90) cc_final: 0.7574 (tpt-90) REVERT: d 92 MET cc_start: 0.8116 (mtp) cc_final: 0.7577 (mmt) REVERT: d 98 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7614 (tm-30) REVERT: d 120 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8257 (tp) REVERT: e 37 LYS cc_start: 0.8356 (ttpp) cc_final: 0.8155 (ttpp) REVERT: e 92 GLN cc_start: 0.8502 (tt0) cc_final: 0.8035 (tt0) REVERT: e 145 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8153 (tt) REVERT: e 147 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7939 (mm) REVERT: f 104 LYS cc_start: 0.9333 (ttmt) cc_final: 0.8731 (ttpp) REVERT: f 106 GLU cc_start: 0.7976 (mp0) cc_final: 0.7637 (mp0) REVERT: f 121 ASN cc_start: 0.9184 (t0) cc_final: 0.8631 (t0) REVERT: f 125 MET cc_start: 0.7311 (pmm) cc_final: 0.7023 (pmm) REVERT: g 38 GLU cc_start: 0.8185 (pm20) cc_final: 0.7799 (pm20) REVERT: g 61 MET cc_start: 0.6608 (tpt) cc_final: 0.5722 (mmm) REVERT: g 73 ASN cc_start: 0.9431 (t0) cc_final: 0.9185 (t0) REVERT: g 82 ARG cc_start: 0.8557 (mmt90) cc_final: 0.8108 (mmt-90) REVERT: g 119 LEU cc_start: 0.9076 (tp) cc_final: 0.8772 (tp) REVERT: m 261 MET cc_start: 0.8573 (mmm) cc_final: 0.8336 (mmm) REVERT: n 259 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7089 (t0) outliers start: 46 outliers final: 31 residues processed: 187 average time/residue: 0.1543 time to fit residues: 36.2237 Evaluate side-chains 189 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 b residue 53 VAL Chi-restraints excluded: chain d residue 35 VAL 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 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 88 SER 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 147 LEU Chi-restraints excluded: chain g residue 97 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 60 GLN ** e 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.135470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.103274 restraints weight = 10198.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.106308 restraints weight = 6986.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.107314 restraints weight = 4654.510| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4468 Z= 0.249 Angle : 0.759 10.332 6051 Z= 0.378 Chirality : 0.043 0.192 721 Planarity : 0.004 0.036 728 Dihedral : 7.104 53.341 658 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 11.20 % Allowed : 34.01 % Favored : 54.79 % 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: -0.51 (0.34), residues: 520 helix: 2.01 (0.32), residues: 222 sheet: -0.96 (0.57), residues: 83 loop : -2.77 (0.30), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP e 59 HIS 0.002 0.001 HIS d 89 PHE 0.021 0.002 PHE g 120 TYR 0.018 0.002 TYR f 149 ARG 0.005 0.001 ARG g 82 *********************** 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 211 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 156 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.5665 (t80) REVERT: a 46 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7300 (tt) REVERT: a 52 ARG cc_start: 0.6726 (ttt180) cc_final: 0.6091 (ttt180) REVERT: b 34 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7245 (mm) REVERT: b 40 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8083 (t80) REVERT: d 63 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8271 (mtp-110) REVERT: d 72 ARG cc_start: 0.7932 (tpt-90) cc_final: 0.7660 (tpt-90) REVERT: d 92 MET cc_start: 0.8244 (mtp) cc_final: 0.7710 (mmt) REVERT: d 98 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7247 (tp30) REVERT: e 92 GLN cc_start: 0.8391 (tt0) cc_final: 0.7931 (tt0) REVERT: e 120 GLU cc_start: 0.7331 (tm-30) cc_final: 0.7087 (tm-30) REVERT: e 145 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8229 (tt) REVERT: e 147 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7851 (mm) REVERT: f 59 TRP cc_start: 0.7877 (m100) cc_final: 0.7407 (m100) REVERT: f 61 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6648 (t70) REVERT: f 104 LYS cc_start: 0.9418 (ttmt) cc_final: 0.8945 (ttpt) REVERT: f 120 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8725 (tm-30) REVERT: f 121 ASN cc_start: 0.9147 (t0) cc_final: 0.8469 (t0) REVERT: f 125 MET cc_start: 0.7447 (pmm) cc_final: 0.7111 (pmm) REVERT: g 73 ASN cc_start: 0.9416 (t0) cc_final: 0.9176 (t0) REVERT: g 119 LEU cc_start: 0.9068 (tp) cc_final: 0.8765 (tp) REVERT: g 129 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8318 (mt) REVERT: m 261 MET cc_start: 0.8685 (mmm) cc_final: 0.8327 (tpt) REVERT: m 272 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7935 (mp) REVERT: n 259 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7393 (t0) outliers start: 55 outliers final: 34 residues processed: 187 average time/residue: 0.1472 time to fit residues: 34.9064 Evaluate side-chains 196 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 32 CYS 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 112 VAL 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 109 ASN m 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.137678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.105701 restraints weight = 9886.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.108967 restraints weight = 6784.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.109954 restraints weight = 4307.513| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4468 Z= 0.200 Angle : 0.735 10.934 6051 Z= 0.365 Chirality : 0.042 0.159 721 Planarity : 0.004 0.030 728 Dihedral : 6.854 54.312 655 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 9.37 % Allowed : 35.85 % Favored : 54.79 % 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: -0.41 (0.35), residues: 520 helix: 2.10 (0.33), residues: 222 sheet: -0.97 (0.57), residues: 83 loop : -2.70 (0.31), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 59 HIS 0.003 0.001 HIS e 61 PHE 0.028 0.002 PHE a 40 TYR 0.012 0.001 TYR d 79 ARG 0.002 0.000 ARG b 52 *********************** 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 206 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.4939 (t80) REVERT: a 46 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7258 (tt) REVERT: a 52 ARG cc_start: 0.6656 (ttt180) cc_final: 0.6025 (ttt180) REVERT: b 34 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7119 (mm) REVERT: b 40 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7857 (t80) REVERT: d 59 ASP cc_start: 0.7746 (p0) cc_final: 0.6767 (t0) REVERT: d 63 ARG cc_start: 0.8997 (ttm170) cc_final: 0.8265 (mtp-110) REVERT: d 92 MET cc_start: 0.8291 (mtp) cc_final: 0.7751 (mmt) REVERT: d 98 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7459 (tm-30) REVERT: e 115 ARG cc_start: 0.8459 (ttm110) cc_final: 0.7799 (ttm110) REVERT: e 145 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8180 (tt) REVERT: e 147 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7875 (mm) REVERT: f 59 TRP cc_start: 0.7648 (m100) cc_final: 0.7222 (m100) REVERT: f 61 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.6405 (t-90) REVERT: f 104 LYS cc_start: 0.9389 (ttmt) cc_final: 0.8977 (ttpp) REVERT: f 106 GLU cc_start: 0.8034 (mp0) cc_final: 0.7788 (mp0) REVERT: f 120 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8631 (tm-30) REVERT: f 121 ASN cc_start: 0.9100 (t0) cc_final: 0.8443 (t0) REVERT: f 125 MET cc_start: 0.7244 (pmm) cc_final: 0.6897 (pmm) REVERT: g 73 ASN cc_start: 0.9435 (t0) cc_final: 0.9135 (t0) REVERT: g 74 LEU cc_start: 0.8796 (tt) cc_final: 0.8311 (mt) REVERT: g 119 LEU cc_start: 0.9093 (tp) cc_final: 0.8787 (tp) REVERT: m 261 MET cc_start: 0.8606 (mmm) cc_final: 0.8198 (tpt) REVERT: m 286 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8163 (tptp) REVERT: n 256 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7273 (tm-30) REVERT: n 259 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7063 (t0) outliers start: 46 outliers final: 27 residues processed: 187 average time/residue: 0.1601 time to fit residues: 37.5379 Evaluate side-chains 186 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 e residue 38 VAL 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 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 42 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 28 optimal weight: 0.0060 chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.136362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.105170 restraints weight = 9948.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.107423 restraints weight = 7335.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.108274 restraints weight = 4854.626| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4468 Z= 0.239 Angle : 0.787 10.710 6051 Z= 0.388 Chirality : 0.043 0.160 721 Planarity : 0.004 0.023 728 Dihedral : 6.783 53.150 655 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 9.98 % Allowed : 37.27 % Favored : 52.75 % 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: -0.45 (0.35), residues: 520 helix: 2.05 (0.32), residues: 222 sheet: -0.98 (0.57), residues: 83 loop : -2.70 (0.32), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP e 59 HIS 0.001 0.001 HIS e 61 PHE 0.025 0.002 PHE g 120 TYR 0.027 0.002 TYR n 276 ARG 0.003 0.000 ARG g 82 *********************** 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: 49 poor density : 155 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6042 (t80) REVERT: a 52 ARG cc_start: 0.6642 (ttt180) cc_final: 0.5926 (ttt180) REVERT: b 34 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7185 (mm) REVERT: b 40 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7884 (t80) REVERT: d 59 ASP cc_start: 0.7733 (p0) cc_final: 0.6733 (t0) REVERT: d 63 ARG cc_start: 0.9015 (ttm170) cc_final: 0.8289 (mtp-110) REVERT: d 92 MET cc_start: 0.8326 (mtp) cc_final: 0.7802 (mmt) REVERT: d 98 GLU cc_start: 0.8075 (tm-30) cc_final: 0.6644 (tm-30) REVERT: e 115 ARG cc_start: 0.8499 (ttm110) cc_final: 0.8183 (ttm110) REVERT: e 145 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8227 (tt) REVERT: e 147 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7878 (mm) REVERT: f 59 TRP cc_start: 0.7699 (m100) cc_final: 0.7046 (m100) REVERT: f 61 HIS cc_start: 0.6986 (OUTLIER) cc_final: 0.6357 (t70) REVERT: f 104 LYS cc_start: 0.9403 (ttmt) cc_final: 0.9123 (ttpt) REVERT: f 110 PHE cc_start: 0.7335 (p90) cc_final: 0.7026 (p90) REVERT: f 117 ARG cc_start: 0.8211 (ptt-90) cc_final: 0.8006 (ptt180) REVERT: f 120 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8635 (tm-30) REVERT: f 121 ASN cc_start: 0.9108 (t0) cc_final: 0.8415 (t0) REVERT: f 125 MET cc_start: 0.7326 (pmm) cc_final: 0.6973 (pmm) REVERT: g 73 ASN cc_start: 0.9470 (t0) cc_final: 0.9206 (t0) REVERT: g 119 LEU cc_start: 0.9082 (tp) cc_final: 0.8776 (tp) REVERT: m 261 MET cc_start: 0.8633 (mmm) cc_final: 0.8205 (tpt) REVERT: m 286 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8220 (tptp) REVERT: n 256 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7388 (tm-30) REVERT: n 259 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7079 (t0) outliers start: 49 outliers final: 34 residues processed: 182 average time/residue: 0.1627 time to fit residues: 36.8354 Evaluate side-chains 191 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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: 3.9990 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 0.0070 chunk 9 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** 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 = 0.4026 r_free = 0.4026 target = 0.137138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.105558 restraints weight = 9827.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108875 restraints weight = 6654.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.109851 restraints weight = 4211.354| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4468 Z= 0.213 Angle : 0.790 10.262 6051 Z= 0.391 Chirality : 0.043 0.152 721 Planarity : 0.003 0.023 728 Dihedral : 6.792 53.020 655 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 7.54 % Allowed : 40.53 % 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: 2.12 (0.33), residues: 222 sheet: -1.00 (0.57), residues: 83 loop : -2.65 (0.33), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 59 HIS 0.003 0.001 HIS e 61 PHE 0.026 0.002 PHE g 120 TYR 0.019 0.001 TYR d 79 ARG 0.002 0.000 ARG b 52 *********************** 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 193 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7108 (OUTLIER) cc_final: 0.6270 (t80) REVERT: a 52 ARG cc_start: 0.6683 (ttt180) cc_final: 0.5948 (ttt180) REVERT: b 34 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7163 (mm) REVERT: b 40 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7815 (t80) REVERT: d 63 ARG cc_start: 0.9017 (ttm170) cc_final: 0.8291 (mtp-110) REVERT: d 72 ARG cc_start: 0.7966 (tpt-90) cc_final: 0.7602 (tpp-160) REVERT: d 92 MET cc_start: 0.8311 (mtp) cc_final: 0.7804 (mmt) REVERT: d 98 GLU cc_start: 0.7982 (tm-30) cc_final: 0.6745 (tm-30) REVERT: e 92 GLN cc_start: 0.8289 (tt0) cc_final: 0.7897 (tt0) REVERT: e 115 ARG cc_start: 0.8502 (ttm110) cc_final: 0.8231 (ttm110) REVERT: e 145 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8225 (tt) REVERT: e 147 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7872 (mm) REVERT: f 61 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.6842 (t-90) REVERT: f 104 LYS cc_start: 0.9386 (ttmt) cc_final: 0.9010 (ttpp) REVERT: f 110 PHE cc_start: 0.7381 (p90) cc_final: 0.7062 (p90) REVERT: f 121 ASN cc_start: 0.9095 (t0) cc_final: 0.8409 (t0) REVERT: f 125 MET cc_start: 0.7249 (pmm) cc_final: 0.6883 (pmm) REVERT: g 73 ASN cc_start: 0.9429 (t0) cc_final: 0.9122 (t0) REVERT: g 74 LEU cc_start: 0.8930 (tt) cc_final: 0.8396 (mt) REVERT: g 119 LEU cc_start: 0.9097 (tp) cc_final: 0.8787 (tp) REVERT: m 261 MET cc_start: 0.8608 (mmm) cc_final: 0.8220 (tpt) REVERT: m 286 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8040 (tptp) REVERT: n 256 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7468 (tm-30) REVERT: n 259 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7112 (t0) outliers start: 37 outliers final: 27 residues processed: 176 average time/residue: 0.1704 time to fit residues: 37.4127 Evaluate side-chains 186 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 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 61 HIS 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 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 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: 0.8980 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** 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 = 0.4010 r_free = 0.4010 target = 0.135972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.104146 restraints weight = 10019.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.107380 restraints weight = 6815.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.108411 restraints weight = 4420.980| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4468 Z= 0.228 Angle : 0.795 9.364 6051 Z= 0.390 Chirality : 0.043 0.156 721 Planarity : 0.004 0.025 728 Dihedral : 6.680 50.711 655 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 8.35 % Allowed : 39.10 % 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: -0.35 (0.35), residues: 520 helix: 2.13 (0.32), residues: 222 sheet: -0.92 (0.58), residues: 83 loop : -2.64 (0.33), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 59 HIS 0.002 0.001 HIS e 61 PHE 0.026 0.002 PHE g 120 TYR 0.017 0.002 TYR g 34 ARG 0.003 0.000 ARG g 82 *********************** 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 192 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6405 (t80) REVERT: a 52 ARG cc_start: 0.6658 (ttt180) cc_final: 0.5971 (ttt180) REVERT: b 34 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7171 (mm) REVERT: b 40 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7836 (t80) REVERT: d 63 ARG cc_start: 0.9000 (ttm170) cc_final: 0.8239 (mtp-110) REVERT: d 72 ARG cc_start: 0.7898 (tpt-90) cc_final: 0.7543 (tpp-160) REVERT: d 92 MET cc_start: 0.8305 (mtp) cc_final: 0.7852 (mmt) REVERT: d 98 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7166 (tm-30) REVERT: e 92 GLN cc_start: 0.8351 (tt0) cc_final: 0.7930 (tt0) REVERT: e 115 ARG cc_start: 0.8522 (ttm110) cc_final: 0.8218 (ttm110) REVERT: e 145 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8244 (tt) REVERT: e 147 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7865 (mm) REVERT: f 61 HIS cc_start: 0.7331 (OUTLIER) cc_final: 0.6989 (t-90) REVERT: f 104 LYS cc_start: 0.9355 (ttmt) cc_final: 0.9016 (ttpp) REVERT: f 110 PHE cc_start: 0.7512 (p90) cc_final: 0.7189 (p90) REVERT: f 121 ASN cc_start: 0.9157 (t0) cc_final: 0.8071 (t0) REVERT: f 125 MET cc_start: 0.7267 (pmm) cc_final: 0.6916 (pmm) REVERT: g 73 ASN cc_start: 0.9430 (t0) cc_final: 0.9121 (t0) REVERT: g 74 LEU cc_start: 0.8898 (tt) cc_final: 0.8402 (mt) REVERT: g 119 LEU cc_start: 0.9081 (tp) cc_final: 0.8748 (tp) REVERT: m 261 MET cc_start: 0.8673 (mmm) cc_final: 0.8212 (tpt) REVERT: m 286 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8159 (tptp) REVERT: n 256 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7519 (tm-30) REVERT: n 259 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7117 (t0) outliers start: 41 outliers final: 30 residues processed: 174 average time/residue: 0.1700 time to fit residues: 36.8951 Evaluate side-chains 188 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 97 VAL 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 129 SER Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 61 HIS 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 136 ILE Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** 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 = 0.4035 r_free = 0.4035 target = 0.137946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.106337 restraints weight = 9779.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.109614 restraints weight = 6607.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.110698 restraints weight = 4214.992| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4468 Z= 0.199 Angle : 0.815 12.473 6051 Z= 0.399 Chirality : 0.043 0.152 721 Planarity : 0.003 0.030 728 Dihedral : 6.737 52.585 655 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.91 % Allowed : 41.55 % 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: -0.24 (0.36), residues: 520 helix: 2.24 (0.33), residues: 222 sheet: -1.04 (0.54), residues: 96 loop : -2.60 (0.33), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 59 HIS 0.003 0.001 HIS e 61 PHE 0.026 0.002 PHE g 120 TYR 0.017 0.001 TYR d 79 ARG 0.002 0.000 ARG b 52 ********************** 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 179 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.5853 (t80) REVERT: a 52 ARG cc_start: 0.6555 (ttt180) cc_final: 0.5966 (ttt180) REVERT: b 34 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7177 (mm) REVERT: b 40 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.7643 (t80) REVERT: d 63 ARG cc_start: 0.8991 (ttm170) cc_final: 0.8213 (mtp-110) REVERT: d 72 ARG cc_start: 0.7945 (tpt-90) cc_final: 0.7592 (tpp-160) REVERT: d 92 MET cc_start: 0.8314 (mtp) cc_final: 0.7847 (mmt) REVERT: d 98 GLU cc_start: 0.7982 (tm-30) cc_final: 0.6756 (tm-30) REVERT: e 92 GLN cc_start: 0.8325 (tt0) cc_final: 0.7929 (tt0) REVERT: e 115 ARG cc_start: 0.8497 (ttm110) cc_final: 0.8203 (ttm110) REVERT: e 124 GLU cc_start: 0.8389 (tp30) cc_final: 0.7680 (pm20) REVERT: e 145 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8204 (tt) REVERT: e 147 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7925 (mm) REVERT: f 104 LYS cc_start: 0.9337 (ttmt) cc_final: 0.8972 (ttpp) REVERT: f 110 PHE cc_start: 0.7534 (p90) cc_final: 0.7237 (p90) REVERT: f 125 MET cc_start: 0.7210 (pmm) cc_final: 0.6843 (pmm) REVERT: g 73 ASN cc_start: 0.9413 (t0) cc_final: 0.9087 (t0) REVERT: g 74 LEU cc_start: 0.8907 (tt) cc_final: 0.8408 (mt) REVERT: g 119 LEU cc_start: 0.9066 (tp) cc_final: 0.8765 (tp) REVERT: m 261 MET cc_start: 0.8575 (mmm) cc_final: 0.8239 (tpt) REVERT: m 286 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7973 (tptp) REVERT: n 256 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7444 (tm-30) REVERT: n 259 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.6908 (t0) outliers start: 29 outliers final: 21 residues processed: 166 average time/residue: 0.1693 time to fit residues: 34.7644 Evaluate side-chains 171 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 114 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU 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 76 SER Chi-restraints excluded: chain g residue 136 ILE 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 274 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** 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 = 0.4021 r_free = 0.4021 target = 0.136515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.104700 restraints weight = 10082.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.107939 restraints weight = 6901.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.108903 restraints weight = 4420.014| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4468 Z= 0.231 Angle : 0.811 8.332 6051 Z= 0.401 Chirality : 0.043 0.151 721 Planarity : 0.004 0.031 728 Dihedral : 6.645 50.642 655 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 6.92 % Allowed : 40.73 % Favored : 52.34 % 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: -0.23 (0.35), residues: 520 helix: 2.26 (0.33), residues: 222 sheet: -1.14 (0.57), residues: 84 loop : -2.50 (0.33), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP e 59 HIS 0.002 0.001 HIS e 61 PHE 0.026 0.002 PHE g 120 TYR 0.021 0.002 TYR d 79 ARG 0.003 0.000 ARG g 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1699.45 seconds wall clock time: 31 minutes 18.75 seconds (1878.75 seconds total)