Starting phenix.real_space_refine on Fri Aug 2 19:13:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/08_2024/8yc0_39128.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/08_2024/8yc0_39128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/08_2024/8yc0_39128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/08_2024/8yc0_39128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/08_2024/8yc0_39128.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/08_2024/8yc0_39128.cif" } resolution = 4.12 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= 0.004 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 3009 2.51 5 N 731 2.21 5 O 858 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 "b TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 59": "OD1" <-> "OD2" Residue "d GLU 98": "OE1" <-> "OE2" Residue "d ASP 100": "OD1" <-> "OD2" Residue "e ASP 63": "OD1" <-> "OD2" Residue "e PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 124": "OE1" <-> "OE2" Residue "f TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 38": "OE1" <-> "OE2" Residue "g ASP 39": "OD1" <-> "OD2" Residue "g PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 80": "OD1" <-> "OD2" Residue "n TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 4635 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 203 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "b" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 218 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} 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: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} 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: "b" 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: 3.25, per 1000 atoms: 0.70 Number of scatterers: 4635 At special positions: 0 Unit cell: (100.004, 86.96, 89.134, 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 858 8.00 N 731 7.00 C 3009 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=2.04 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=2.04 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: 1.82 Conformation dependent library (CDL) restraints added in 827.8 milliseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1084 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 40.0% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'a' and resid 26 through 50 removed outlier: 4.043A pdb=" N LYS a 30 " --> pdb=" O LEU a 26 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU a 31 " --> pdb=" O LEU a 27 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR a 33 " --> pdb=" O PRO a 29 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU a 34 " --> pdb=" O LYS a 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 54 Processing helix chain 'd' and resid 100 through 124 removed outlier: 3.620A pdb=" N VAL d 104 " --> pdb=" O ASP d 100 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA d 105 " --> pdb=" O PRO d 101 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY d 106 " --> pdb=" O ALA d 102 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 152 removed outlier: 3.538A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 154 removed outlier: 3.517A pdb=" N ASN f 154 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 removed outlier: 3.921A pdb=" N ASP g 80 " --> pdb=" O ASN g 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 137 removed outlier: 3.694A pdb=" N SER g 116 " --> pdb=" O ALA g 112 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY g 117 " --> pdb=" O ALA g 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 257 through 289 removed outlier: 3.582A pdb=" N MET m 261 " --> pdb=" O GLU m 257 " (cutoff:3.500A) Processing helix chain 'n' and resid 253 through 288 Processing sheet with id=AA1, first strand: chain 'd' and resid 32 through 35 removed outlier: 7.525A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU d 60 " --> pdb=" O VAL d 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 41 through 46 removed outlier: 3.843A pdb=" N VAL d 44 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL e 97 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR e 99 " --> pdb=" O LEU e 58 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU e 58 " --> pdb=" O TYR e 99 " (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 41 removed outlier: 3.705A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY e 76 " --> pdb=" O SER e 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 38 removed outlier: 4.006A pdb=" N LYS f 37 " --> pdb=" O THR f 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR f 48 " --> pdb=" O LYS f 37 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU f 82 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 112 through 115 removed outlier: 5.591A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.960A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 54 through 57 removed outlier: 6.318A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE g 62 " --> pdb=" O TRP g 55 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 648 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: 1.11 Time building geometry restraints manager: 2.00 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: 1433 1.34 - 1.47: 1125 1.47 - 1.59: 2115 1.59 - 1.71: 0 1.71 - 1.83: 51 Bond restraints: 4724 Sorted by residual: bond pdb=" C ASP a 28 " pdb=" N PRO a 29 " ideal model delta sigma weight residual 1.333 1.364 -0.031 1.44e-02 4.82e+03 4.62e+00 bond pdb=" CA ASP e 63 " pdb=" CB ASP e 63 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.69e-02 3.50e+03 1.55e+00 bond pdb=" CB PRO f 100 " pdb=" CG PRO f 100 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.46e+00 bond pdb=" N ASN e 121 " pdb=" CA ASN e 121 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.17e+00 bond pdb=" CB ASP f 137 " pdb=" CG ASP f 137 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 ... (remaining 4719 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.75: 69 105.75 - 112.82: 2565 112.82 - 119.89: 1543 119.89 - 126.96: 2189 126.96 - 134.02: 38 Bond angle restraints: 6404 Sorted by residual: angle pdb=" C LEU a 27 " pdb=" CA LEU a 27 " pdb=" CB LEU a 27 " ideal model delta sigma weight residual 115.89 109.41 6.48 1.32e+00 5.74e-01 2.41e+01 angle pdb=" CA CYS f 49 " pdb=" CB CYS f 49 " pdb=" SG CYS f 49 " ideal model delta sigma weight residual 114.40 123.14 -8.74 2.30e+00 1.89e-01 1.44e+01 angle pdb=" CA LEU f 114 " pdb=" CB LEU f 114 " pdb=" CG LEU f 114 " ideal model delta sigma weight residual 116.30 129.15 -12.85 3.50e+00 8.16e-02 1.35e+01 angle pdb=" N GLY d 46 " pdb=" CA GLY d 46 " pdb=" C GLY d 46 " ideal model delta sigma weight residual 111.56 115.25 -3.69 1.01e+00 9.80e-01 1.33e+01 angle pdb=" CB MET m 262 " pdb=" CG MET m 262 " pdb=" SD MET m 262 " ideal model delta sigma weight residual 112.70 123.09 -10.39 3.00e+00 1.11e-01 1.20e+01 ... (remaining 6399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 2343 16.69 - 33.39: 390 33.39 - 50.08: 118 50.08 - 66.78: 20 66.78 - 83.47: 6 Dihedral angle restraints: 2877 sinusoidal: 1184 harmonic: 1693 Sorted by residual: 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 93.00 175.13 -82.13 1 1.00e+01 1.00e-02 8.28e+01 dihedral pdb=" CB CYS e 49 " pdb=" SG CYS e 49 " pdb=" SG CYS e 98 " pdb=" CB CYS e 98 " ideal model delta sinusoidal sigma weight residual -86.00 -15.84 -70.16 1 1.00e+01 1.00e-02 6.34e+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 -154.55 68.55 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 2874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 504 0.037 - 0.074: 174 0.074 - 0.111: 55 0.111 - 0.148: 16 0.148 - 0.186: 2 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA ASP e 63 " pdb=" N ASP e 63 " pdb=" C ASP e 63 " pdb=" CB ASP e 63 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA ILE d 70 " pdb=" N ILE d 70 " pdb=" C ILE d 70 " pdb=" CB ILE d 70 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ASN e 121 " pdb=" N ASN e 121 " pdb=" C ASN e 121 " pdb=" CB ASN e 121 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 748 not shown) Planarity restraints: 785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR f 99 " 0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO f 100 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO f 100 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO f 100 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR e 99 " 0.037 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO e 100 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO e 100 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO e 100 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS f 104 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO f 105 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO f 105 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO f 105 " 0.017 5.00e-02 4.00e+02 ... (remaining 782 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 95 2.67 - 3.23: 4543 3.23 - 3.79: 7049 3.79 - 4.34: 8421 4.34 - 4.90: 13883 Nonbonded interactions: 33991 Sorted by model distance: nonbonded pdb=" OD1 ASP e 126 " pdb=" N VAL e 127 " model vdw 2.114 3.120 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.225 3.040 nonbonded pdb=" N GLU f 56 " pdb=" OE1 GLU f 56 " model vdw 2.255 3.120 nonbonded pdb=" NE2 GLN e 60 " pdb=" OD1 ASN e 65 " model vdw 2.258 3.120 nonbonded pdb=" O ILE d 24 " pdb=" OH TYR e 95 " model vdw 2.279 3.040 ... (remaining 33986 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' and resid 28 through 50) selection = (chain 'b' and resid 28 through 50) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 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: 0.440 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.160 Find NCS groups from input model: 0.140 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 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 0.060 4724 Z= 0.224 Angle : 0.774 12.853 6404 Z= 0.389 Chirality : 0.043 0.186 751 Planarity : 0.005 0.086 785 Dihedral : 17.513 83.473 1766 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.58 % Allowed : 39.73 % Favored : 59.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.95 (0.34), residues: 565 helix: 2.06 (0.33), residues: 212 sheet: -1.22 (0.64), residues: 74 loop : -2.81 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 43 HIS 0.004 0.001 HIS f 61 PHE 0.020 0.001 PHE g 118 TYR 0.016 0.001 TYR b 42 ARG 0.005 0.000 ARG d 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 71 TYR cc_start: 0.7273 (m-80) cc_final: 0.6834 (m-10) REVERT: d 90 TYR cc_start: 0.7388 (m-80) cc_final: 0.6902 (m-80) REVERT: e 36 TYR cc_start: 0.6981 (m-80) cc_final: 0.5299 (m-10) REVERT: e 46 ILE cc_start: 0.8085 (mp) cc_final: 0.7838 (mm) REVERT: e 47 LEU cc_start: 0.8296 (mt) cc_final: 0.8084 (tt) REVERT: e 49 CYS cc_start: 0.6913 (t) cc_final: 0.5597 (t) REVERT: e 85 LYS cc_start: 0.7718 (mptt) cc_final: 0.7517 (mptt) REVERT: e 91 GLU cc_start: 0.8234 (tp30) cc_final: 0.8019 (tm-30) REVERT: e 92 GLN cc_start: 0.7710 (tt0) cc_final: 0.7193 (tt0) REVERT: e 117 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7622 (ttt180) REVERT: e 120 GLU cc_start: 0.8013 (pp20) cc_final: 0.7719 (pp20) REVERT: e 123 MET cc_start: 0.5173 (mtt) cc_final: 0.4753 (ptp) REVERT: g 38 GLU cc_start: 0.8295 (pm20) cc_final: 0.8071 (pm20) REVERT: g 43 LEU cc_start: 0.7667 (mt) cc_final: 0.7448 (mt) REVERT: g 80 ASP cc_start: 0.8028 (m-30) cc_final: 0.7779 (t0) REVERT: g 111 ASN cc_start: 0.7321 (m110) cc_final: 0.6954 (p0) REVERT: m 286 LYS cc_start: 0.7448 (tppt) cc_final: 0.7238 (tptt) outliers start: 3 outliers final: 0 residues processed: 154 average time/residue: 0.1913 time to fit residues: 35.8210 Evaluate side-chains 136 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 21 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4724 Z= 0.236 Angle : 0.682 6.033 6404 Z= 0.358 Chirality : 0.044 0.169 751 Planarity : 0.005 0.057 785 Dihedral : 5.059 50.680 692 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.19 % Allowed : 3.88 % Favored : 95.93 % 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: -1.01 (0.34), residues: 565 helix: 2.09 (0.33), residues: 217 sheet: -1.32 (0.64), residues: 75 loop : -2.99 (0.29), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 59 HIS 0.007 0.001 HIS f 61 PHE 0.023 0.002 PHE b 40 TYR 0.011 0.002 TYR n 264 ARG 0.003 0.001 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 71 TYR cc_start: 0.7279 (m-80) cc_final: 0.6962 (m-10) REVERT: d 87 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7414 (tm-30) REVERT: e 36 TYR cc_start: 0.7549 (m-80) cc_final: 0.5704 (m-80) REVERT: e 49 CYS cc_start: 0.7378 (t) cc_final: 0.5901 (t) REVERT: e 90 LEU cc_start: 0.8708 (mm) cc_final: 0.8419 (mm) REVERT: e 115 ARG cc_start: 0.7216 (mmm-85) cc_final: 0.6893 (tpt170) REVERT: e 117 ARG cc_start: 0.7716 (mtp180) cc_final: 0.7473 (ttt180) REVERT: e 120 GLU cc_start: 0.7884 (pp20) cc_final: 0.7658 (pp20) REVERT: e 126 ASP cc_start: 0.8226 (t0) cc_final: 0.7994 (t0) REVERT: f 106 GLU cc_start: 0.7842 (tt0) cc_final: 0.7480 (tt0) REVERT: f 115 ARG cc_start: 0.7755 (ttt180) cc_final: 0.7466 (ttt-90) REVERT: f 120 GLU cc_start: 0.8897 (tt0) cc_final: 0.8433 (tm-30) REVERT: f 121 ASN cc_start: 0.7920 (m-40) cc_final: 0.6612 (m-40) REVERT: f 124 GLU cc_start: 0.8501 (tt0) cc_final: 0.8034 (tp30) REVERT: f 125 MET cc_start: 0.8766 (ppp) cc_final: 0.8409 (ppp) REVERT: f 128 MET cc_start: 0.6149 (mpp) cc_final: 0.5733 (mmt) REVERT: g 39 ASP cc_start: 0.9184 (p0) cc_final: 0.8902 (p0) REVERT: g 79 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7958 (mtmt) REVERT: g 125 SER cc_start: 0.8822 (t) cc_final: 0.8560 (t) REVERT: m 284 THR cc_start: 0.9164 (m) cc_final: 0.8922 (m) REVERT: n 259 ASN cc_start: 0.7297 (OUTLIER) cc_final: 0.6849 (t0) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.1738 time to fit residues: 36.2284 Evaluate side-chains 138 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- 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** n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4724 Z= 0.178 Angle : 0.633 7.592 6404 Z= 0.327 Chirality : 0.043 0.186 751 Planarity : 0.005 0.055 785 Dihedral : 4.945 51.040 692 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.34), residues: 565 helix: 2.35 (0.33), residues: 217 sheet: -1.25 (0.62), residues: 78 loop : -2.87 (0.30), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 43 HIS 0.006 0.001 HIS d 89 PHE 0.031 0.001 PHE b 40 TYR 0.013 0.001 TYR g 34 ARG 0.006 0.001 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 71 TYR cc_start: 0.7235 (m-80) cc_final: 0.6857 (m-10) REVERT: d 87 GLN cc_start: 0.7228 (tm-30) cc_final: 0.6987 (tm-30) REVERT: e 36 TYR cc_start: 0.7496 (m-80) cc_final: 0.6052 (m-80) REVERT: e 49 CYS cc_start: 0.7621 (t) cc_final: 0.6564 (t) REVERT: e 90 LEU cc_start: 0.8656 (mm) cc_final: 0.8439 (mm) REVERT: e 98 CYS cc_start: 0.5284 (p) cc_final: 0.4727 (p) REVERT: e 115 ARG cc_start: 0.7298 (mmm-85) cc_final: 0.6919 (tpt90) REVERT: e 117 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7462 (ttt180) REVERT: e 126 ASP cc_start: 0.8212 (t0) cc_final: 0.7882 (t0) REVERT: f 106 GLU cc_start: 0.7954 (tt0) cc_final: 0.7631 (tt0) REVERT: f 115 ARG cc_start: 0.7713 (ttt180) cc_final: 0.7078 (tpt-90) REVERT: f 120 GLU cc_start: 0.8891 (tt0) cc_final: 0.8609 (tm-30) REVERT: f 124 GLU cc_start: 0.8353 (tt0) cc_final: 0.8002 (tp30) REVERT: f 125 MET cc_start: 0.8820 (ppp) cc_final: 0.8412 (ppp) REVERT: f 128 MET cc_start: 0.6081 (mpp) cc_final: 0.5536 (mmt) REVERT: g 39 ASP cc_start: 0.9204 (p0) cc_final: 0.8882 (p0) REVERT: g 80 ASP cc_start: 0.8283 (t0) cc_final: 0.8068 (t0) REVERT: g 95 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8173 (mtpp) REVERT: g 118 PHE cc_start: 0.8261 (t80) cc_final: 0.7848 (t80) REVERT: g 125 SER cc_start: 0.8757 (t) cc_final: 0.8474 (t) REVERT: m 284 THR cc_start: 0.9100 (m) cc_final: 0.8839 (m) REVERT: n 265 MET cc_start: 0.7481 (tpp) cc_final: 0.7007 (ttm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1772 time to fit residues: 34.6093 Evaluate side-chains 135 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 92 GLN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4724 Z= 0.196 Angle : 0.643 6.342 6404 Z= 0.335 Chirality : 0.043 0.173 751 Planarity : 0.004 0.050 785 Dihedral : 4.920 48.843 692 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.34), residues: 565 helix: 2.22 (0.33), residues: 218 sheet: -0.73 (0.71), residues: 66 loop : -2.83 (0.30), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP f 59 HIS 0.004 0.001 HIS f 61 PHE 0.031 0.001 PHE b 40 TYR 0.017 0.001 TYR e 99 ARG 0.006 0.001 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 45 GLU cc_start: 0.7212 (mp0) cc_final: 0.6963 (mp0) REVERT: d 68 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6871 (mtp180) REVERT: d 70 ILE cc_start: 0.8318 (mt) cc_final: 0.7608 (tt) REVERT: d 71 TYR cc_start: 0.7162 (m-80) cc_final: 0.6878 (m-10) REVERT: e 36 TYR cc_start: 0.7591 (m-80) cc_final: 0.6243 (m-80) REVERT: e 49 CYS cc_start: 0.7657 (t) cc_final: 0.6743 (t) REVERT: e 90 LEU cc_start: 0.8722 (mm) cc_final: 0.8342 (mm) REVERT: e 98 CYS cc_start: 0.5631 (p) cc_final: 0.5116 (p) REVERT: e 115 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.6755 (tpt90) REVERT: e 117 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7639 (ttt180) REVERT: e 126 ASP cc_start: 0.8229 (t0) cc_final: 0.8006 (t0) REVERT: f 106 GLU cc_start: 0.7960 (tt0) cc_final: 0.7624 (tt0) REVERT: f 115 ARG cc_start: 0.7735 (ttt180) cc_final: 0.7110 (tpt-90) REVERT: f 120 GLU cc_start: 0.8901 (tt0) cc_final: 0.8456 (tm-30) REVERT: f 121 ASN cc_start: 0.7965 (m-40) cc_final: 0.6638 (m-40) REVERT: f 124 GLU cc_start: 0.8339 (tt0) cc_final: 0.8028 (tp30) REVERT: f 125 MET cc_start: 0.8733 (ppp) cc_final: 0.8421 (ppp) REVERT: f 126 ASP cc_start: 0.7666 (t0) cc_final: 0.7402 (t0) REVERT: f 128 MET cc_start: 0.6144 (mpp) cc_final: 0.5588 (mmt) REVERT: g 34 TYR cc_start: 0.7447 (t80) cc_final: 0.7224 (t80) REVERT: g 39 ASP cc_start: 0.9134 (p0) cc_final: 0.8789 (p0) REVERT: g 79 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7972 (mtmt) REVERT: g 80 ASP cc_start: 0.8257 (t0) cc_final: 0.8025 (t0) REVERT: g 95 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8084 (mtpp) REVERT: g 118 PHE cc_start: 0.8231 (t80) cc_final: 0.7864 (t80) REVERT: m 284 THR cc_start: 0.9090 (m) cc_final: 0.8818 (m) REVERT: n 265 MET cc_start: 0.7573 (tpp) cc_final: 0.7185 (ttm) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1824 time to fit residues: 33.4372 Evaluate side-chains 125 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4724 Z= 0.234 Angle : 0.667 7.045 6404 Z= 0.343 Chirality : 0.043 0.187 751 Planarity : 0.004 0.049 785 Dihedral : 5.020 49.922 692 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: -0.70 (0.34), residues: 565 helix: 2.16 (0.33), residues: 218 sheet: -0.72 (0.66), residues: 73 loop : -2.79 (0.30), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 72 HIS 0.005 0.001 HIS f 61 PHE 0.010 0.001 PHE n 277 TYR 0.010 0.001 TYR e 99 ARG 0.006 0.001 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 68 ARG cc_start: 0.7536 (mtp180) cc_final: 0.7102 (mtp180) REVERT: d 70 ILE cc_start: 0.8363 (mt) cc_final: 0.7532 (tt) REVERT: d 71 TYR cc_start: 0.7221 (m-80) cc_final: 0.6874 (m-10) REVERT: e 36 TYR cc_start: 0.7651 (m-80) cc_final: 0.6305 (m-80) REVERT: e 49 CYS cc_start: 0.7665 (t) cc_final: 0.6765 (t) REVERT: e 90 LEU cc_start: 0.8788 (mm) cc_final: 0.8529 (mm) REVERT: e 98 CYS cc_start: 0.5584 (p) cc_final: 0.4773 (p) REVERT: e 117 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7719 (ttt180) REVERT: f 46 ILE cc_start: 0.8278 (mm) cc_final: 0.8058 (mm) REVERT: f 89 GLU cc_start: 0.7544 (tt0) cc_final: 0.7279 (tt0) REVERT: f 106 GLU cc_start: 0.7859 (tt0) cc_final: 0.7638 (tt0) REVERT: f 115 ARG cc_start: 0.7738 (ttt180) cc_final: 0.7139 (tpt-90) REVERT: f 120 GLU cc_start: 0.8942 (tt0) cc_final: 0.8589 (tm-30) REVERT: f 124 GLU cc_start: 0.8371 (tt0) cc_final: 0.8129 (tp30) REVERT: f 128 MET cc_start: 0.5901 (mpp) cc_final: 0.5333 (mmt) REVERT: g 39 ASP cc_start: 0.9010 (p0) cc_final: 0.8681 (p0) REVERT: g 43 LEU cc_start: 0.7784 (mp) cc_final: 0.7514 (mt) REVERT: g 80 ASP cc_start: 0.8138 (t0) cc_final: 0.7908 (t0) REVERT: g 118 PHE cc_start: 0.8296 (t80) cc_final: 0.7739 (t80) REVERT: m 267 LEU cc_start: 0.7978 (tt) cc_final: 0.7680 (tp) REVERT: m 284 THR cc_start: 0.9120 (m) cc_final: 0.8842 (m) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1789 time to fit residues: 32.5245 Evaluate side-chains 125 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4724 Z= 0.195 Angle : 0.643 6.426 6404 Z= 0.331 Chirality : 0.043 0.183 751 Planarity : 0.004 0.047 785 Dihedral : 5.004 51.105 692 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % 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: -0.69 (0.35), residues: 565 helix: 2.14 (0.33), residues: 220 sheet: -1.25 (0.57), residues: 93 loop : -2.66 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP f 59 HIS 0.009 0.002 HIS g 29 PHE 0.011 0.001 PHE n 277 TYR 0.007 0.001 TYR f 111 ARG 0.010 0.001 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 70 ILE cc_start: 0.8391 (mt) cc_final: 0.7732 (tt) REVERT: d 71 TYR cc_start: 0.7078 (m-80) cc_final: 0.6762 (m-10) REVERT: d 87 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7288 (tm-30) REVERT: e 36 TYR cc_start: 0.7685 (m-80) cc_final: 0.6395 (m-80) REVERT: e 49 CYS cc_start: 0.7646 (t) cc_final: 0.6739 (t) REVERT: e 90 LEU cc_start: 0.8635 (mm) cc_final: 0.8369 (mm) REVERT: e 98 CYS cc_start: 0.5561 (p) cc_final: 0.4704 (p) REVERT: e 115 ARG cc_start: 0.8009 (tpt170) cc_final: 0.7003 (tpt170) REVERT: e 117 ARG cc_start: 0.8043 (mtp180) cc_final: 0.7777 (ttt180) REVERT: f 46 ILE cc_start: 0.8256 (mm) cc_final: 0.8003 (mm) REVERT: f 89 GLU cc_start: 0.7915 (tt0) cc_final: 0.7210 (tt0) REVERT: f 106 GLU cc_start: 0.7898 (tt0) cc_final: 0.7657 (tt0) REVERT: f 115 ARG cc_start: 0.7726 (ttt180) cc_final: 0.7221 (tpt-90) REVERT: f 120 GLU cc_start: 0.8970 (tt0) cc_final: 0.8650 (tm-30) REVERT: f 124 GLU cc_start: 0.8336 (tt0) cc_final: 0.8075 (tp30) REVERT: f 125 MET cc_start: 0.8546 (ppp) cc_final: 0.8165 (ppp) REVERT: f 128 MET cc_start: 0.5978 (mpp) cc_final: 0.5377 (mmt) REVERT: g 39 ASP cc_start: 0.8961 (p0) cc_final: 0.8648 (p0) REVERT: g 43 LEU cc_start: 0.7803 (mp) cc_final: 0.7481 (mt) REVERT: g 79 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8018 (mtmt) REVERT: g 80 ASP cc_start: 0.7999 (t0) cc_final: 0.7351 (t0) REVERT: g 82 ARG cc_start: 0.8383 (ptp-170) cc_final: 0.7932 (ptp-170) REVERT: g 118 PHE cc_start: 0.8293 (t80) cc_final: 0.7713 (t80) REVERT: m 267 LEU cc_start: 0.7944 (tt) cc_final: 0.7665 (tp) REVERT: m 284 THR cc_start: 0.9104 (m) cc_final: 0.8832 (m) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1697 time to fit residues: 30.2415 Evaluate side-chains 121 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 92 GLN f 81 HIS n 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4724 Z= 0.183 Angle : 0.641 6.906 6404 Z= 0.327 Chirality : 0.042 0.163 751 Planarity : 0.004 0.043 785 Dihedral : 4.995 51.060 692 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.35), residues: 565 helix: 2.23 (0.33), residues: 220 sheet: -0.30 (0.70), residues: 67 loop : -2.57 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 59 HIS 0.005 0.001 HIS g 29 PHE 0.010 0.001 PHE b 40 TYR 0.017 0.001 TYR b 42 ARG 0.005 0.001 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 70 ILE cc_start: 0.8354 (mt) cc_final: 0.7753 (tt) REVERT: d 87 GLN cc_start: 0.7381 (tm-30) cc_final: 0.7082 (tm-30) REVERT: e 36 TYR cc_start: 0.7708 (m-80) cc_final: 0.6417 (m-80) REVERT: e 49 CYS cc_start: 0.7664 (t) cc_final: 0.6886 (t) REVERT: e 90 LEU cc_start: 0.8741 (mm) cc_final: 0.8418 (mm) REVERT: e 98 CYS cc_start: 0.5568 (p) cc_final: 0.4692 (p) REVERT: e 115 ARG cc_start: 0.7901 (tpt170) cc_final: 0.7251 (tpt170) REVERT: f 46 ILE cc_start: 0.8181 (mm) cc_final: 0.7929 (mm) REVERT: f 106 GLU cc_start: 0.7933 (tt0) cc_final: 0.7630 (tt0) REVERT: f 115 ARG cc_start: 0.7607 (ttt180) cc_final: 0.7286 (tpt-90) REVERT: f 120 GLU cc_start: 0.8950 (tt0) cc_final: 0.8545 (tm-30) REVERT: f 124 GLU cc_start: 0.8388 (tt0) cc_final: 0.8122 (tp30) REVERT: f 125 MET cc_start: 0.8499 (ppp) cc_final: 0.8136 (ppp) REVERT: f 128 MET cc_start: 0.5986 (mpp) cc_final: 0.5369 (mmt) REVERT: g 39 ASP cc_start: 0.8964 (p0) cc_final: 0.8668 (p0) REVERT: g 43 LEU cc_start: 0.7748 (mp) cc_final: 0.7471 (mt) REVERT: g 79 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8006 (mtmt) REVERT: g 80 ASP cc_start: 0.7930 (t0) cc_final: 0.7272 (t0) REVERT: g 82 ARG cc_start: 0.8693 (ptp-170) cc_final: 0.8193 (ptp-170) REVERT: g 118 PHE cc_start: 0.8238 (t80) cc_final: 0.7747 (t80) REVERT: m 267 LEU cc_start: 0.7887 (tt) cc_final: 0.7579 (tp) REVERT: m 284 THR cc_start: 0.9083 (m) cc_final: 0.8799 (m) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1692 time to fit residues: 29.5884 Evaluate side-chains 122 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.0060 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 38 optimal weight: 5.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN f 81 HIS n 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4724 Z= 0.175 Angle : 0.650 7.377 6404 Z= 0.331 Chirality : 0.042 0.163 751 Planarity : 0.004 0.042 785 Dihedral : 4.998 51.622 692 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.34 (0.35), residues: 565 helix: 2.37 (0.33), residues: 218 sheet: -0.44 (0.65), residues: 75 loop : -2.53 (0.31), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 55 HIS 0.005 0.001 HIS g 29 PHE 0.010 0.001 PHE n 277 TYR 0.007 0.001 TYR g 100 ARG 0.006 0.001 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 68 ARG cc_start: 0.7326 (mtp-110) cc_final: 0.7044 (mtp-110) REVERT: d 70 ILE cc_start: 0.8153 (mt) cc_final: 0.7661 (tt) REVERT: d 87 GLN cc_start: 0.7269 (tm-30) cc_final: 0.6965 (tm-30) REVERT: e 36 TYR cc_start: 0.6954 (m-80) cc_final: 0.5887 (m-10) REVERT: e 49 CYS cc_start: 0.7510 (t) cc_final: 0.7098 (t) REVERT: f 46 ILE cc_start: 0.8092 (mm) cc_final: 0.7830 (mm) REVERT: f 89 GLU cc_start: 0.7913 (tt0) cc_final: 0.7203 (tt0) REVERT: f 101 ARG cc_start: 0.7562 (mtp85) cc_final: 0.7269 (mmm-85) REVERT: f 106 GLU cc_start: 0.7913 (tt0) cc_final: 0.7645 (tt0) REVERT: f 115 ARG cc_start: 0.7611 (ttt180) cc_final: 0.6932 (tpt-90) REVERT: f 121 ASN cc_start: 0.7763 (m-40) cc_final: 0.7367 (m-40) REVERT: f 124 GLU cc_start: 0.8376 (tt0) cc_final: 0.8116 (tp30) REVERT: f 125 MET cc_start: 0.8530 (ppp) cc_final: 0.8217 (ppp) REVERT: f 128 MET cc_start: 0.5970 (mpp) cc_final: 0.5356 (mmt) REVERT: g 39 ASP cc_start: 0.8947 (p0) cc_final: 0.8631 (p0) REVERT: g 43 LEU cc_start: 0.7707 (mp) cc_final: 0.7486 (mt) REVERT: g 61 MET cc_start: 0.1489 (tpt) cc_final: 0.0724 (tpt) REVERT: g 79 LYS cc_start: 0.8319 (mtpt) cc_final: 0.7992 (mtmt) REVERT: g 80 ASP cc_start: 0.7740 (t0) cc_final: 0.7176 (t0) REVERT: g 82 ARG cc_start: 0.8706 (ptp-170) cc_final: 0.8184 (ptp-170) REVERT: g 118 PHE cc_start: 0.8208 (t80) cc_final: 0.7715 (t80) REVERT: m 267 LEU cc_start: 0.7912 (tt) cc_final: 0.7602 (tp) REVERT: m 284 THR cc_start: 0.9031 (m) cc_final: 0.8774 (m) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1648 time to fit residues: 29.3443 Evaluate side-chains 120 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.0470 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.0060 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 92 GLN f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4724 Z= 0.179 Angle : 0.662 7.594 6404 Z= 0.334 Chirality : 0.042 0.160 751 Planarity : 0.004 0.042 785 Dihedral : 5.015 51.623 692 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 565 helix: 2.39 (0.33), residues: 218 sheet: -0.89 (0.62), residues: 81 loop : -2.54 (0.32), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 55 HIS 0.004 0.001 HIS g 29 PHE 0.016 0.001 PHE b 40 TYR 0.021 0.001 TYR b 42 ARG 0.003 0.001 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 68 ARG cc_start: 0.7332 (mtp-110) cc_final: 0.6885 (mtp-110) REVERT: d 70 ILE cc_start: 0.8012 (mt) cc_final: 0.7689 (tt) REVERT: d 87 GLN cc_start: 0.7151 (tm-30) cc_final: 0.6689 (tm-30) REVERT: e 36 TYR cc_start: 0.7004 (m-80) cc_final: 0.5308 (m-80) REVERT: e 49 CYS cc_start: 0.7528 (t) cc_final: 0.6603 (t) REVERT: e 98 CYS cc_start: 0.5303 (p) cc_final: 0.4948 (p) REVERT: f 46 ILE cc_start: 0.8026 (mm) cc_final: 0.7687 (mm) REVERT: f 81 HIS cc_start: 0.6474 (t-170) cc_final: 0.6262 (t70) REVERT: f 101 ARG cc_start: 0.7939 (mtp85) cc_final: 0.7664 (mmt-90) REVERT: f 106 GLU cc_start: 0.7880 (tt0) cc_final: 0.7577 (tt0) REVERT: f 115 ARG cc_start: 0.7730 (ttt180) cc_final: 0.7076 (tpt-90) REVERT: f 121 ASN cc_start: 0.7775 (m-40) cc_final: 0.7368 (m-40) REVERT: f 124 GLU cc_start: 0.8336 (tt0) cc_final: 0.8090 (tp30) REVERT: f 125 MET cc_start: 0.8528 (ppp) cc_final: 0.8238 (ppp) REVERT: f 128 MET cc_start: 0.5947 (mpp) cc_final: 0.5342 (mmt) REVERT: g 39 ASP cc_start: 0.8923 (p0) cc_final: 0.8617 (p0) REVERT: g 79 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8008 (mppt) REVERT: g 80 ASP cc_start: 0.7667 (t0) cc_final: 0.7124 (t0) REVERT: g 82 ARG cc_start: 0.8690 (ptp-170) cc_final: 0.8178 (ptp-170) REVERT: g 118 PHE cc_start: 0.8170 (t80) cc_final: 0.7723 (t80) REVERT: m 267 LEU cc_start: 0.7891 (tt) cc_final: 0.7587 (tp) REVERT: m 284 THR cc_start: 0.9002 (m) cc_final: 0.8735 (m) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1683 time to fit residues: 29.8463 Evaluate side-chains 122 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 92 GLN ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4724 Z= 0.413 Angle : 0.857 8.448 6404 Z= 0.439 Chirality : 0.050 0.174 751 Planarity : 0.005 0.039 785 Dihedral : 5.644 47.793 692 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.34), residues: 565 helix: 1.57 (0.32), residues: 220 sheet: -1.55 (0.53), residues: 99 loop : -2.82 (0.32), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 55 HIS 0.008 0.002 HIS f 61 PHE 0.020 0.002 PHE n 277 TYR 0.020 0.002 TYR f 111 ARG 0.007 0.001 ARG d 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 24 ILE cc_start: 0.6608 (pt) cc_final: 0.6386 (pt) REVERT: d 68 ARG cc_start: 0.7664 (mtp-110) cc_final: 0.7212 (mtp-110) REVERT: e 36 TYR cc_start: 0.7103 (m-80) cc_final: 0.5110 (m-80) REVERT: e 49 CYS cc_start: 0.7663 (t) cc_final: 0.5964 (t) REVERT: e 89 GLU cc_start: 0.8134 (tt0) cc_final: 0.7928 (tt0) REVERT: e 90 LEU cc_start: 0.8583 (mm) cc_final: 0.8282 (mm) REVERT: e 115 ARG cc_start: 0.8233 (tpt170) cc_final: 0.7509 (tpt90) REVERT: f 106 GLU cc_start: 0.7898 (tt0) cc_final: 0.7548 (tt0) REVERT: f 121 ASN cc_start: 0.7831 (m-40) cc_final: 0.7385 (m-40) REVERT: f 124 GLU cc_start: 0.8628 (tt0) cc_final: 0.8276 (tp30) REVERT: f 125 MET cc_start: 0.8592 (ppp) cc_final: 0.8311 (ppp) REVERT: f 128 MET cc_start: 0.6124 (mpp) cc_final: 0.5486 (mmt) REVERT: g 39 ASP cc_start: 0.8952 (p0) cc_final: 0.8628 (p0) REVERT: g 79 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8086 (mtmt) REVERT: g 118 PHE cc_start: 0.8245 (t80) cc_final: 0.7665 (t80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1517 time to fit residues: 26.9629 Evaluate side-chains 116 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN f 81 HIS ** n 259 ASN ** 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 = 0.4004 r_free = 0.4004 target = 0.164168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143846 restraints weight = 7861.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143278 restraints weight = 11778.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144052 restraints weight = 10092.055| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4724 Z= 0.213 Angle : 0.717 7.078 6404 Z= 0.367 Chirality : 0.044 0.171 751 Planarity : 0.004 0.040 785 Dihedral : 5.333 49.350 692 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: -0.77 (0.34), residues: 565 helix: 1.96 (0.32), residues: 217 sheet: -1.03 (0.58), residues: 85 loop : -2.63 (0.32), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP f 59 HIS 0.004 0.001 HIS g 29 PHE 0.014 0.001 PHE m 288 TYR 0.010 0.001 TYR g 100 ARG 0.004 0.001 ARG f 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1352.81 seconds wall clock time: 24 minutes 33.46 seconds (1473.46 seconds total)