Starting phenix.real_space_refine on Fri Aug 2 18:35:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/08_2024/8wxe_37904.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/08_2024/8wxe_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/08_2024/8wxe_37904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/08_2024/8wxe_37904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/08_2024/8wxe_37904.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/08_2024/8wxe_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 Residue "a PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 124": "OE1" <-> "OE2" Residue "f GLU 86": "OE1" <-> "OE2" Residue "f GLU 89": "OE1" <-> "OE2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "g PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 257": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 3.15, 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 - 3.50 Amino acid : False - 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: 1.72 Conformation dependent library (CDL) restraints added in 751.0 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: 0.45 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: 1.04 Time building geometry restraints manager: 1.86 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: 97.67 - 104.94: 57 104.94 - 112.21: 2286 112.21 - 119.47: 1402 119.47 - 126.74: 2266 126.74 - 134.00: 40 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: 0.370 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.380 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 0.516 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: 0.1526 time to fit residues: 41.8880 Evaluate side-chains 164 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 fitting. rotamer outliers: 48 poor density : 168 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 30 LYS cc_start: 0.8469 (tmmt) cc_final: 0.7970 (mmtm) REVERT: a 46 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7288 (tt) REVERT: a 52 ARG cc_start: 0.6697 (ttt180) cc_final: 0.6277 (ttt180) REVERT: b 34 LEU cc_start: 0.8020 (tt) cc_final: 0.7320 (mm) REVERT: d 63 ARG cc_start: 0.8998 (ttm170) cc_final: 0.8246 (mtp-110) REVERT: d 72 ARG cc_start: 0.7665 (tpt-90) cc_final: 0.7211 (tpt-90) REVERT: d 92 MET cc_start: 0.8513 (mtp) cc_final: 0.7944 (mmt) REVERT: d 97 VAL cc_start: 0.8954 (t) cc_final: 0.8686 (p) REVERT: d 98 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7464 (tm-30) REVERT: d 120 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8388 (tp) REVERT: e 92 GLN cc_start: 0.8630 (tt0) cc_final: 0.8262 (tt0) REVERT: e 145 LEU cc_start: 0.8589 (mm) cc_final: 0.8064 (tt) REVERT: e 147 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7981 (mm) REVERT: f 106 GLU cc_start: 0.8381 (mp0) cc_final: 0.8168 (mp0) REVERT: f 121 ASN cc_start: 0.9204 (t0) cc_final: 0.8716 (t0) REVERT: f 125 MET cc_start: 0.7309 (pmm) cc_final: 0.7093 (pmm) REVERT: g 34 TYR cc_start: 0.8630 (t80) cc_final: 0.8334 (t80) REVERT: g 38 GLU cc_start: 0.8053 (pm20) cc_final: 0.7501 (pm20) REVERT: g 73 ASN cc_start: 0.9477 (t0) cc_final: 0.9244 (t0) REVERT: g 82 ARG cc_start: 0.8878 (mmt90) cc_final: 0.8431 (mmt-90) REVERT: g 111 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8624 (p0) REVERT: g 119 LEU cc_start: 0.9120 (tp) cc_final: 0.8808 (tp) REVERT: m 272 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8557 (mp) REVERT: n 259 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.7739 (t0) outliers start: 48 outliers final: 28 residues processed: 196 average time/residue: 0.1474 time to fit residues: 36.3165 Evaluate side-chains 189 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 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 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 25 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3618 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= 0.197 Angle : 0.742 9.708 6051 Z= 0.368 Chirality : 0.042 0.154 721 Planarity : 0.004 0.059 728 Dihedral : 7.469 58.065 658 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 8.76 % Allowed : 37.27 % Favored : 53.97 % 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: -0.28 (0.35), residues: 520 helix: 2.29 (0.32), residues: 221 sheet: -0.96 (0.61), residues: 71 loop : -2.62 (0.32), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP e 59 HIS 0.002 0.001 HIS f 61 PHE 0.020 0.002 PHE g 120 TYR 0.022 0.002 TYR e 36 ARG 0.009 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 209 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 166 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 46 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7117 (tt) REVERT: a 52 ARG cc_start: 0.6689 (ttt180) cc_final: 0.6201 (ttt180) REVERT: b 34 LEU cc_start: 0.7988 (tt) cc_final: 0.7300 (mm) REVERT: d 63 ARG cc_start: 0.9008 (ttm170) cc_final: 0.8311 (mtp-110) REVERT: d 72 ARG cc_start: 0.7700 (tpt-90) cc_final: 0.7383 (tpt-90) REVERT: d 92 MET cc_start: 0.8474 (mtp) cc_final: 0.7903 (mmt) REVERT: d 97 VAL cc_start: 0.8938 (t) cc_final: 0.8528 (p) REVERT: d 98 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8223 (tm-30) REVERT: d 120 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8228 (tp) REVERT: e 92 GLN cc_start: 0.8597 (tt0) cc_final: 0.8114 (tt0) REVERT: e 123 MET cc_start: 0.8252 (pmm) cc_final: 0.8051 (pmm) REVERT: e 126 ASP cc_start: 0.7670 (t0) cc_final: 0.7459 (t0) REVERT: e 145 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8106 (tt) REVERT: e 147 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7886 (mm) REVERT: f 61 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.7033 (t70) REVERT: f 104 LYS cc_start: 0.9322 (ttmt) cc_final: 0.8809 (tmmt) REVERT: f 106 GLU cc_start: 0.8248 (mp0) cc_final: 0.7948 (mp0) REVERT: f 120 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8713 (tm-30) REVERT: f 121 ASN cc_start: 0.9214 (t0) cc_final: 0.8664 (t0) REVERT: f 125 MET cc_start: 0.7349 (pmm) cc_final: 0.7086 (pmm) REVERT: g 34 TYR cc_start: 0.8702 (t80) cc_final: 0.8476 (t80) REVERT: g 61 MET cc_start: 0.7038 (tpt) cc_final: 0.6252 (mmm) REVERT: g 73 ASN cc_start: 0.9448 (t0) cc_final: 0.9188 (t0) REVERT: g 111 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8555 (p0) REVERT: g 119 LEU cc_start: 0.9072 (tp) cc_final: 0.8793 (tp) REVERT: n 259 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.7710 (t0) outliers start: 43 outliers final: 20 residues processed: 190 average time/residue: 0.1511 time to fit residues: 36.1019 Evaluate side-chains 183 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 g residue 97 LEU Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL 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 34 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 60 GLN f 61 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4468 Z= 0.223 Angle : 0.735 9.650 6051 Z= 0.365 Chirality : 0.043 0.194 721 Planarity : 0.004 0.046 728 Dihedral : 7.259 55.525 658 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 10.18 % Allowed : 35.23 % 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: -0.37 (0.34), residues: 520 helix: 2.15 (0.32), residues: 223 sheet: -0.98 (0.61), residues: 71 loop : -2.65 (0.30), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP e 59 HIS 0.007 0.001 HIS f 61 PHE 0.038 0.002 PHE e 110 TYR 0.018 0.002 TYR e 36 ARG 0.004 0.001 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 210 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 160 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 46 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7111 (tt) REVERT: a 52 ARG cc_start: 0.6706 (ttt180) cc_final: 0.6142 (ttt180) REVERT: b 34 LEU cc_start: 0.7975 (tt) cc_final: 0.7304 (mm) REVERT: d 63 ARG cc_start: 0.8995 (ttm170) cc_final: 0.8275 (mtp-110) REVERT: d 72 ARG cc_start: 0.7731 (tpt-90) cc_final: 0.7457 (tpt-90) REVERT: d 92 MET cc_start: 0.8534 (mtp) cc_final: 0.7871 (mmt) REVERT: d 98 GLU cc_start: 0.8504 (tm-30) cc_final: 0.6999 (tm-30) REVERT: d 120 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8297 (tp) REVERT: e 92 GLN cc_start: 0.8518 (tt0) cc_final: 0.8005 (tt0) REVERT: e 126 ASP cc_start: 0.7640 (t0) cc_final: 0.7392 (t0) REVERT: e 145 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8148 (tt) REVERT: e 147 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7939 (mm) REVERT: f 104 LYS cc_start: 0.9350 (ttmt) cc_final: 0.8518 (ttpp) REVERT: f 121 ASN cc_start: 0.9189 (t0) cc_final: 0.8603 (t0) REVERT: f 125 MET cc_start: 0.7336 (pmm) cc_final: 0.7084 (pmm) REVERT: g 34 TYR cc_start: 0.8669 (t80) cc_final: 0.8360 (t80) REVERT: g 38 GLU cc_start: 0.8137 (pm20) cc_final: 0.7763 (pm20) REVERT: g 73 ASN cc_start: 0.9449 (t0) cc_final: 0.9224 (t0) REVERT: g 111 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8550 (p0) REVERT: g 119 LEU cc_start: 0.9087 (tp) cc_final: 0.8772 (tp) REVERT: m 272 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8298 (mp) REVERT: n 259 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.7833 (t0) outliers start: 50 outliers final: 33 residues processed: 190 average time/residue: 0.1483 time to fit residues: 35.4233 Evaluate side-chains 192 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 111 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4468 Z= 0.210 Angle : 0.737 10.760 6051 Z= 0.363 Chirality : 0.042 0.175 721 Planarity : 0.004 0.035 728 Dihedral : 7.137 54.473 658 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 9.78 % Allowed : 35.64 % 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: -0.48 (0.34), residues: 520 helix: 2.14 (0.32), residues: 220 sheet: -1.08 (0.56), residues: 83 loop : -2.77 (0.30), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP e 59 HIS 0.002 0.001 HIS d 89 PHE 0.020 0.002 PHE g 120 TYR 0.017 0.001 TYR e 36 ARG 0.003 0.001 ARG b 52 *********************** 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 207 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 159 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.4934 (t80) REVERT: a 46 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7154 (tt) REVERT: a 52 ARG cc_start: 0.6735 (ttt180) cc_final: 0.6139 (ttt180) REVERT: b 34 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7227 (mm) REVERT: b 40 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8146 (t80) REVERT: d 63 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8273 (mtp-110) REVERT: d 72 ARG cc_start: 0.7793 (tpt-90) cc_final: 0.7559 (tpt-90) REVERT: d 92 MET cc_start: 0.8569 (mtp) cc_final: 0.7982 (mmt) REVERT: d 98 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7642 (tm-30) REVERT: d 120 LEU cc_start: 0.8455 (tt) cc_final: 0.8234 (tp) REVERT: e 87 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8228 (t80) REVERT: e 92 GLN cc_start: 0.8397 (tt0) cc_final: 0.7907 (tt0) REVERT: e 115 ARG cc_start: 0.8401 (ttm110) cc_final: 0.7713 (ttm110) REVERT: e 126 ASP cc_start: 0.7560 (t0) cc_final: 0.7316 (t70) REVERT: e 145 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8166 (tt) REVERT: e 147 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7913 (mm) REVERT: f 61 HIS cc_start: 0.6656 (OUTLIER) cc_final: 0.6234 (t70) REVERT: f 104 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8916 (ttpp) REVERT: f 120 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8771 (tm-30) REVERT: f 121 ASN cc_start: 0.9219 (t0) cc_final: 0.8564 (t0) REVERT: f 125 MET cc_start: 0.7321 (pmm) cc_final: 0.7024 (pmm) REVERT: g 34 TYR cc_start: 0.8686 (t80) cc_final: 0.8376 (t80) REVERT: g 73 ASN cc_start: 0.9452 (t0) cc_final: 0.9221 (t0) REVERT: g 82 ARG cc_start: 0.8726 (mmt90) cc_final: 0.8215 (mmt-90) REVERT: g 111 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8523 (p0) REVERT: g 119 LEU cc_start: 0.9088 (tp) cc_final: 0.8773 (tp) REVERT: g 129 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8344 (mt) REVERT: m 272 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8227 (mp) REVERT: n 259 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.7636 (t0) outliers start: 48 outliers final: 31 residues processed: 186 average time/residue: 0.1580 time to fit residues: 37.1272 Evaluate side-chains 199 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 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 d residue 116 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER 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 111 ASN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4468 Z= 0.188 Angle : 0.737 10.870 6051 Z= 0.365 Chirality : 0.042 0.158 721 Planarity : 0.004 0.029 728 Dihedral : 6.815 54.652 655 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 9.98 % Allowed : 36.25 % Favored : 53.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.34), residues: 520 helix: 2.12 (0.32), residues: 222 sheet: -1.09 (0.59), residues: 71 loop : -2.67 (0.31), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP e 59 HIS 0.002 0.001 HIS e 61 PHE 0.030 0.002 PHE a 40 TYR 0.014 0.001 TYR e 36 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 209 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 160 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.4978 (t80) REVERT: a 52 ARG cc_start: 0.6837 (ttt180) cc_final: 0.6167 (ttt180) REVERT: b 34 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7163 (mm) REVERT: b 40 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8028 (t80) REVERT: d 63 ARG cc_start: 0.9004 (ttm170) cc_final: 0.8251 (mtp-110) REVERT: d 92 MET cc_start: 0.8596 (mtp) cc_final: 0.8038 (mmt) REVERT: d 98 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7228 (tm-30) REVERT: e 109 ASN cc_start: 0.5422 (OUTLIER) cc_final: 0.5096 (m-40) REVERT: e 115 ARG cc_start: 0.8406 (ttm110) cc_final: 0.7712 (ttm110) REVERT: e 126 ASP cc_start: 0.7582 (t0) cc_final: 0.7299 (t0) REVERT: e 145 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8118 (tt) REVERT: e 147 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7861 (mm) REVERT: f 61 HIS cc_start: 0.6686 (OUTLIER) cc_final: 0.6288 (t70) REVERT: f 104 LYS cc_start: 0.9325 (ttmt) cc_final: 0.8906 (ttpp) REVERT: f 106 GLU cc_start: 0.8283 (mp0) cc_final: 0.8003 (mp0) REVERT: f 110 PHE cc_start: 0.6996 (p90) cc_final: 0.6584 (p90) REVERT: f 120 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8652 (tm-30) REVERT: f 121 ASN cc_start: 0.9184 (t0) cc_final: 0.8534 (t0) REVERT: f 125 MET cc_start: 0.7183 (pmm) cc_final: 0.6876 (pmm) REVERT: g 34 TYR cc_start: 0.8687 (t80) cc_final: 0.8401 (t80) REVERT: g 73 ASN cc_start: 0.9436 (t0) cc_final: 0.9127 (t0) REVERT: g 74 LEU cc_start: 0.8829 (tt) cc_final: 0.8291 (mt) REVERT: g 111 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8552 (p0) REVERT: g 119 LEU cc_start: 0.9080 (tp) cc_final: 0.8772 (tp) REVERT: m 286 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8048 (tptp) REVERT: n 259 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7506 (t0) outliers start: 49 outliers final: 29 residues processed: 187 average time/residue: 0.1509 time to fit residues: 35.4379 Evaluate side-chains 192 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR 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 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 d residue 116 LEU 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 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 42 VAL Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain g residue 126 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 27 optimal weight: 0.0870 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4468 Z= 0.276 Angle : 0.812 11.506 6051 Z= 0.400 Chirality : 0.043 0.175 721 Planarity : 0.004 0.022 728 Dihedral : 6.761 52.975 655 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 10.18 % Allowed : 36.86 % Favored : 52.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.34), residues: 520 helix: 2.00 (0.32), residues: 222 sheet: -1.36 (0.54), residues: 85 loop : -2.66 (0.32), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP e 59 HIS 0.003 0.001 HIS d 89 PHE 0.020 0.002 PHE g 120 TYR 0.027 0.002 TYR d 79 ARG 0.005 0.001 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 213 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 163 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6653 (t80) REVERT: a 52 ARG cc_start: 0.6782 (ttt180) cc_final: 0.6028 (ttt180) REVERT: b 34 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7405 (mm) REVERT: b 40 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8122 (t80) REVERT: b 42 TYR cc_start: 0.7624 (t80) cc_final: 0.7419 (t80) REVERT: d 63 ARG cc_start: 0.9045 (ttm170) cc_final: 0.8338 (mtp-110) REVERT: d 72 ARG cc_start: 0.7796 (tpt-90) cc_final: 0.7507 (tpp80) REVERT: d 92 MET cc_start: 0.8625 (mtp) cc_final: 0.8095 (mmt) REVERT: d 98 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7426 (tm-30) REVERT: e 92 GLN cc_start: 0.8401 (tt0) cc_final: 0.7910 (tt0) REVERT: e 126 ASP cc_start: 0.7746 (t0) cc_final: 0.7453 (t0) REVERT: e 145 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8206 (tt) REVERT: e 147 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7803 (mm) REVERT: f 59 TRP cc_start: 0.7509 (m100) cc_final: 0.6678 (m100) REVERT: f 61 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6228 (t70) REVERT: f 104 LYS cc_start: 0.9349 (ttmt) cc_final: 0.8973 (ttpt) REVERT: f 120 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8698 (tm-30) REVERT: f 121 ASN cc_start: 0.9187 (t0) cc_final: 0.8479 (t0) REVERT: f 125 MET cc_start: 0.7437 (pmm) cc_final: 0.7094 (pmm) REVERT: g 34 TYR cc_start: 0.8711 (t80) cc_final: 0.8453 (t80) REVERT: g 73 ASN cc_start: 0.9497 (t0) cc_final: 0.9240 (t0) REVERT: g 111 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8578 (p0) REVERT: g 119 LEU cc_start: 0.9087 (tp) cc_final: 0.8775 (tp) REVERT: m 272 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8320 (mp) REVERT: m 286 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8332 (tptp) REVERT: n 259 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.7694 (t0) outliers start: 50 outliers final: 35 residues processed: 189 average time/residue: 0.1578 time to fit residues: 37.3870 Evaluate side-chains 198 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 153 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 112 VAL 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 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 61 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 111 ASN 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4468 Z= 0.251 Angle : 0.817 9.809 6051 Z= 0.404 Chirality : 0.043 0.153 721 Planarity : 0.003 0.021 728 Dihedral : 6.834 52.620 655 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 9.57 % Allowed : 38.49 % 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: -0.47 (0.35), residues: 520 helix: 2.03 (0.32), residues: 220 sheet: -1.17 (0.55), residues: 83 loop : -2.58 (0.33), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP e 59 HIS 0.002 0.001 HIS f 61 PHE 0.027 0.002 PHE g 120 TYR 0.019 0.002 TYR d 79 ARG 0.003 0.001 ARG g 82 *********************** 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 205 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 158 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6784 (t80) REVERT: a 52 ARG cc_start: 0.6873 (ttt180) cc_final: 0.6089 (ttt180) REVERT: b 34 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7368 (mm) REVERT: b 40 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8047 (t80) REVERT: d 63 ARG cc_start: 0.9019 (ttm170) cc_final: 0.8277 (mtp-110) REVERT: d 72 ARG cc_start: 0.7832 (tpt-90) cc_final: 0.7535 (tpp-160) REVERT: d 92 MET cc_start: 0.8668 (mtp) cc_final: 0.8143 (mmt) REVERT: d 98 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7546 (tm-30) REVERT: e 92 GLN cc_start: 0.8360 (tt0) cc_final: 0.7931 (tt0) REVERT: e 110 PHE cc_start: 0.7913 (t80) cc_final: 0.7710 (t80) REVERT: e 126 ASP cc_start: 0.7774 (t0) cc_final: 0.7521 (t70) REVERT: e 145 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8221 (tt) REVERT: e 147 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7837 (mm) REVERT: f 61 HIS cc_start: 0.7040 (OUTLIER) cc_final: 0.6738 (t-90) REVERT: f 104 LYS cc_start: 0.9328 (ttmt) cc_final: 0.8963 (ttpp) REVERT: f 110 PHE cc_start: 0.7303 (p90) cc_final: 0.6899 (p90) REVERT: f 120 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8663 (tm-30) REVERT: f 121 ASN cc_start: 0.9179 (t0) cc_final: 0.8388 (t0) REVERT: f 125 MET cc_start: 0.7316 (pmm) cc_final: 0.7008 (pmm) REVERT: g 34 TYR cc_start: 0.8716 (t80) cc_final: 0.8443 (t80) REVERT: g 73 ASN cc_start: 0.9445 (t0) cc_final: 0.9204 (t0) REVERT: g 111 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8591 (p0) REVERT: g 119 LEU cc_start: 0.9115 (tp) cc_final: 0.8751 (tp) REVERT: m 257 GLU cc_start: 0.8079 (mp0) cc_final: 0.7808 (mp0) REVERT: m 286 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8261 (tptp) REVERT: n 259 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.7762 (t0) outliers start: 47 outliers final: 35 residues processed: 184 average time/residue: 0.1757 time to fit residues: 40.1909 Evaluate side-chains 196 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 152 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 112 VAL 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 129 SER Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 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 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 40 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 chunk 29 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4468 Z= 0.213 Angle : 0.816 10.069 6051 Z= 0.396 Chirality : 0.042 0.155 721 Planarity : 0.003 0.024 728 Dihedral : 6.763 52.454 655 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 8.55 % Allowed : 39.51 % 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: -0.41 (0.35), residues: 520 helix: 2.08 (0.33), residues: 220 sheet: -1.08 (0.55), residues: 83 loop : -2.57 (0.32), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP e 59 HIS 0.003 0.001 HIS e 61 PHE 0.038 0.002 PHE a 40 TYR 0.019 0.001 TYR d 79 ARG 0.002 0.000 ARG f 115 *********************** 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 199 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.6462 (t80) REVERT: a 52 ARG cc_start: 0.6742 (ttt180) cc_final: 0.6108 (ttt180) REVERT: b 34 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7276 (mm) REVERT: b 40 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8027 (t80) REVERT: d 63 ARG cc_start: 0.8996 (ttm170) cc_final: 0.8212 (mtp-110) REVERT: d 72 ARG cc_start: 0.7815 (tpt-90) cc_final: 0.7517 (tpp-160) REVERT: d 92 MET cc_start: 0.8611 (mtp) cc_final: 0.8075 (mmt) REVERT: d 98 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7634 (tm-30) REVERT: e 92 GLN cc_start: 0.8357 (tt0) cc_final: 0.7922 (tt0) REVERT: e 126 ASP cc_start: 0.7771 (t0) cc_final: 0.7521 (t70) REVERT: e 145 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8197 (tt) REVERT: e 147 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7837 (mm) REVERT: f 104 LYS cc_start: 0.9295 (ttmt) cc_final: 0.8944 (ttpp) REVERT: f 110 PHE cc_start: 0.7371 (p90) cc_final: 0.6953 (p90) REVERT: f 121 ASN cc_start: 0.9174 (t0) cc_final: 0.8459 (t0) REVERT: f 125 MET cc_start: 0.7262 (pmm) cc_final: 0.6930 (pmm) REVERT: g 34 TYR cc_start: 0.8703 (t80) cc_final: 0.8378 (t80) REVERT: g 73 ASN cc_start: 0.9479 (t0) cc_final: 0.9151 (t0) REVERT: g 74 LEU cc_start: 0.8913 (tt) cc_final: 0.8387 (mt) REVERT: g 111 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8581 (p0) REVERT: g 119 LEU cc_start: 0.9075 (tp) cc_final: 0.8776 (tp) REVERT: m 286 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8132 (tptp) REVERT: n 256 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7489 (tm-30) REVERT: n 259 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.7536 (t0) outliers start: 42 outliers final: 30 residues processed: 181 average time/residue: 0.1540 time to fit residues: 34.7515 Evaluate side-chains 188 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 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 46 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 76 SER 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 256 THR Chi-restraints excluded: chain m residue 266 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4468 Z= 0.209 Angle : 0.823 10.543 6051 Z= 0.399 Chirality : 0.042 0.154 721 Planarity : 0.003 0.027 728 Dihedral : 6.700 51.668 655 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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: -0.33 (0.35), residues: 520 helix: 2.12 (0.33), residues: 220 sheet: -0.90 (0.62), residues: 71 loop : -2.50 (0.32), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP e 59 HIS 0.002 0.001 HIS e 61 PHE 0.026 0.002 PHE g 120 TYR 0.018 0.001 TYR n 276 ARG 0.004 0.000 ARG e 115 ********************** 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 189 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 152 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6392 (t80) REVERT: a 52 ARG cc_start: 0.6713 (ttt180) cc_final: 0.6082 (ttt180) REVERT: b 34 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7196 (mm) REVERT: b 40 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8043 (t80) REVERT: d 63 ARG cc_start: 0.8998 (ttm170) cc_final: 0.8219 (mtp-110) REVERT: d 72 ARG cc_start: 0.7799 (tpt-90) cc_final: 0.7500 (tpp-160) REVERT: d 92 MET cc_start: 0.8599 (mtp) cc_final: 0.8108 (mmt) REVERT: e 92 GLN cc_start: 0.8338 (tt0) cc_final: 0.7903 (tt0) REVERT: e 126 ASP cc_start: 0.7764 (t0) cc_final: 0.7560 (t70) REVERT: e 145 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8161 (tt) REVERT: e 147 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7834 (mm) REVERT: f 104 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8899 (ttpp) REVERT: f 110 PHE cc_start: 0.7459 (p90) cc_final: 0.7058 (p90) REVERT: f 121 ASN cc_start: 0.9255 (t0) cc_final: 0.8207 (t0) REVERT: f 125 MET cc_start: 0.7201 (pmm) cc_final: 0.6885 (pmm) REVERT: g 34 TYR cc_start: 0.8728 (t80) cc_final: 0.8373 (t80) REVERT: g 73 ASN cc_start: 0.9457 (t0) cc_final: 0.9156 (t0) REVERT: g 111 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8486 (p0) REVERT: g 119 LEU cc_start: 0.9073 (tp) cc_final: 0.8734 (tp) REVERT: m 286 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8030 (tptp) REVERT: n 256 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7472 (tm-30) REVERT: n 259 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.7508 (t0) outliers start: 37 outliers final: 28 residues processed: 173 average time/residue: 0.1621 time to fit residues: 35.3610 Evaluate side-chains 185 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 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 84 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 42 VAL 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 256 THR Chi-restraints excluded: chain m residue 266 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3985 r_free = 0.3985 target = 0.133830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.101964 restraints weight = 9981.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.105276 restraints weight = 6863.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.106195 restraints weight = 4432.758| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5578 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= 0.263 Angle : 0.851 10.151 6051 Z= 0.417 Chirality : 0.043 0.150 721 Planarity : 0.004 0.029 728 Dihedral : 6.677 50.567 655 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 9.16 % Allowed : 39.51 % Favored : 51.32 % 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: 2.04 (0.32), residues: 222 sheet: -1.12 (0.55), residues: 90 loop : -2.38 (0.34), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP e 59 HIS 0.001 0.001 HIS f 61 PHE 0.027 0.002 PHE g 120 TYR 0.019 0.002 TYR d 79 ARG 0.004 0.000 ARG g 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1328.96 seconds wall clock time: 24 minutes 19.31 seconds (1459.31 seconds total)