Starting phenix.real_space_refine on Thu Jul 18 23:21:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/07_2024/8yc0_39128.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/07_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_39128/07_2024/8yc0_39128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/07_2024/8yc0_39128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/07_2024/8yc0_39128.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yc0_39128/07_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-5388/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: 3.20, per 1000 atoms: 0.69 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: 1.74 Conformation dependent library (CDL) restraints added in 938.7 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: 0.47 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: 1.07 Time building geometry restraints manager: 1.94 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 2.520 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.225 2.440 nonbonded pdb=" N GLU f 56 " pdb=" OE1 GLU f 56 " model vdw 2.255 2.520 nonbonded pdb=" NE2 GLN e 60 " pdb=" OD1 ASN e 65 " model vdw 2.258 2.520 nonbonded pdb=" O ILE d 24 " pdb=" OH TYR e 95 " model vdw 2.279 2.440 ... (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 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.970 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.650 ------------------------------------------------------------------------------- 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 : 0.535 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: 0.1926 time to fit residues: 35.9801 Evaluate side-chains 136 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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: 3.9990 chunk 40 optimal weight: 0.0870 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.0000 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- 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: 0.6309 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4724 Z= 0.217 Angle : 0.672 5.850 6404 Z= 0.349 Chirality : 0.044 0.172 751 Planarity : 0.005 0.055 785 Dihedral : 5.026 51.236 692 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.19 % Allowed : 3.68 % Favored : 96.12 % 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: -0.96 (0.34), residues: 565 helix: 2.22 (0.33), residues: 215 sheet: -1.66 (0.57), residues: 88 loop : -2.90 (0.30), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 59 HIS 0.007 0.002 HIS f 61 PHE 0.012 0.001 PHE b 40 TYR 0.010 0.001 TYR d 79 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 164 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 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: 0.6986 (m-80) cc_final: 0.6692 (m-10) REVERT: e 49 CYS cc_start: 0.7131 (t) cc_final: 0.5962 (t) REVERT: e 89 GLU cc_start: 0.7606 (tt0) cc_final: 0.7024 (tm-30) REVERT: e 90 LEU cc_start: 0.8720 (mm) cc_final: 0.8031 (mm) REVERT: e 91 GLU cc_start: 0.8344 (tp30) cc_final: 0.8132 (tm-30) REVERT: e 98 CYS cc_start: 0.4214 (p) cc_final: 0.3815 (p) REVERT: e 115 ARG cc_start: 0.7305 (mmm-85) cc_final: 0.6698 (ttm-80) REVERT: e 117 ARG cc_start: 0.7599 (mtp180) cc_final: 0.7341 (ttt180) REVERT: e 120 GLU cc_start: 0.7839 (pp20) cc_final: 0.7605 (pp20) REVERT: f 106 GLU cc_start: 0.7919 (tt0) cc_final: 0.7713 (tt0) REVERT: f 115 ARG cc_start: 0.7657 (ttt180) cc_final: 0.7423 (ttt-90) REVERT: f 120 GLU cc_start: 0.8869 (tt0) cc_final: 0.8439 (tm-30) REVERT: f 121 ASN cc_start: 0.7916 (m-40) cc_final: 0.6612 (m-40) REVERT: f 128 MET cc_start: 0.6076 (mpp) cc_final: 0.5664 (mmt) REVERT: g 39 ASP cc_start: 0.9228 (p0) cc_final: 0.8944 (p0) REVERT: g 95 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8057 (mtpp) REVERT: g 118 PHE cc_start: 0.8196 (t80) cc_final: 0.7631 (t80) REVERT: g 125 SER cc_start: 0.8783 (t) cc_final: 0.8508 (t) REVERT: m 284 THR cc_start: 0.9159 (m) cc_final: 0.8912 (m) REVERT: n 259 ASN cc_start: 0.7224 (OUTLIER) cc_final: 0.6815 (t0) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1790 time to fit residues: 36.1225 Evaluate side-chains 137 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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: 3.9990 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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: 0.6320 moved from start: 0.3004 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= 0.176 Angle : 0.622 7.156 6404 Z= 0.321 Chirality : 0.042 0.185 751 Planarity : 0.005 0.054 785 Dihedral : 4.914 50.643 692 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.64 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: -0.72 (0.35), residues: 565 helix: 2.50 (0.33), residues: 215 sheet: -1.35 (0.59), residues: 86 loop : -2.91 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 43 HIS 0.005 0.001 HIS d 89 PHE 0.033 0.001 PHE b 40 TYR 0.017 0.001 TYR e 99 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 156 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 45 GLU cc_start: 0.6785 (mp0) cc_final: 0.6580 (mp0) REVERT: d 71 TYR cc_start: 0.7166 (m-80) cc_final: 0.6817 (m-10) REVERT: e 49 CYS cc_start: 0.7588 (t) cc_final: 0.6963 (t) REVERT: e 98 CYS cc_start: 0.4954 (p) cc_final: 0.4283 (p) REVERT: e 117 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7463 (ttt180) REVERT: f 89 GLU cc_start: 0.8154 (tt0) cc_final: 0.7394 (tt0) REVERT: f 106 GLU cc_start: 0.7875 (tt0) cc_final: 0.7493 (tt0) REVERT: f 115 ARG cc_start: 0.7587 (ttt180) cc_final: 0.6990 (tpt-90) REVERT: f 120 GLU cc_start: 0.8880 (tt0) cc_final: 0.8613 (tm-30) REVERT: f 124 GLU cc_start: 0.8362 (tt0) cc_final: 0.8120 (tp30) REVERT: f 128 MET cc_start: 0.6017 (mpp) cc_final: 0.5482 (mmt) REVERT: g 39 ASP cc_start: 0.9225 (p0) cc_final: 0.8900 (p0) REVERT: g 79 LYS cc_start: 0.8243 (mtpt) cc_final: 0.8001 (mtmt) REVERT: g 80 ASP cc_start: 0.8300 (t0) cc_final: 0.7948 (t0) REVERT: g 95 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7915 (mtpp) REVERT: g 118 PHE cc_start: 0.8014 (t80) cc_final: 0.7773 (t80) REVERT: g 125 SER cc_start: 0.8763 (t) cc_final: 0.8482 (t) REVERT: m 284 THR cc_start: 0.9103 (m) cc_final: 0.8834 (m) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1840 time to fit residues: 35.4178 Evaluate side-chains 130 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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: 3.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.6372 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4724 Z= 0.195 Angle : 0.628 6.481 6404 Z= 0.324 Chirality : 0.042 0.177 751 Planarity : 0.004 0.048 785 Dihedral : 4.846 48.911 692 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % 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: -0.67 (0.34), residues: 565 helix: 2.39 (0.33), residues: 218 sheet: -1.19 (0.65), residues: 76 loop : -2.82 (0.30), residues: 271 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 0.035 0.001 PHE b 40 TYR 0.011 0.001 TYR e 99 ARG 0.005 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 153 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 68 ARG cc_start: 0.7114 (mtp180) cc_final: 0.6721 (mtp180) REVERT: d 70 ILE cc_start: 0.8326 (mt) cc_final: 0.7623 (tt) REVERT: d 71 TYR cc_start: 0.7183 (m-80) cc_final: 0.6821 (m-10) REVERT: d 87 GLN cc_start: 0.7409 (tm-30) cc_final: 0.7004 (tm-30) REVERT: e 49 CYS cc_start: 0.7500 (t) cc_final: 0.6814 (t) REVERT: e 91 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7694 (tm-30) REVERT: e 98 CYS cc_start: 0.5009 (p) cc_final: 0.4262 (p) REVERT: e 117 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7651 (ttt180) REVERT: f 106 GLU cc_start: 0.7865 (tt0) cc_final: 0.7481 (tt0) REVERT: f 115 ARG cc_start: 0.7552 (ttt180) cc_final: 0.7039 (tpt-90) REVERT: f 120 GLU cc_start: 0.8896 (tt0) cc_final: 0.8457 (tm-30) REVERT: f 121 ASN cc_start: 0.7966 (m-40) cc_final: 0.6601 (m-40) REVERT: f 124 GLU cc_start: 0.8389 (tt0) cc_final: 0.8028 (tp30) REVERT: f 128 MET cc_start: 0.6166 (mpp) cc_final: 0.5571 (mmt) REVERT: g 39 ASP cc_start: 0.9174 (p0) cc_final: 0.8933 (p0) REVERT: g 79 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7965 (mtmt) REVERT: g 80 ASP cc_start: 0.8274 (t0) cc_final: 0.7920 (t0) REVERT: g 118 PHE cc_start: 0.8192 (t80) cc_final: 0.7860 (t80) REVERT: m 284 THR cc_start: 0.9090 (m) cc_final: 0.8819 (m) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1829 time to fit residues: 34.4644 Evaluate side-chains 130 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 0.0000 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6306 moved from start: 0.3603 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= 0.165 Angle : 0.609 6.398 6404 Z= 0.312 Chirality : 0.042 0.175 751 Planarity : 0.004 0.041 785 Dihedral : 4.918 54.424 692 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: -0.50 (0.35), residues: 565 helix: 2.58 (0.33), residues: 217 sheet: -1.11 (0.64), residues: 76 loop : -2.74 (0.30), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP f 59 HIS 0.002 0.000 HIS f 61 PHE 0.010 0.001 PHE b 40 TYR 0.015 0.001 TYR g 34 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 152 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 45 GLU cc_start: 0.7263 (mp0) cc_final: 0.6980 (mp0) REVERT: d 68 ARG cc_start: 0.7230 (mtp180) cc_final: 0.6744 (mtp180) REVERT: d 70 ILE cc_start: 0.8270 (mt) cc_final: 0.7583 (tt) REVERT: d 71 TYR cc_start: 0.7042 (m-80) cc_final: 0.6783 (m-10) REVERT: d 87 GLN cc_start: 0.7225 (tm-30) cc_final: 0.7005 (tm-30) REVERT: d 92 MET cc_start: 0.8679 (mtt) cc_final: 0.8462 (mtt) REVERT: e 49 CYS cc_start: 0.7560 (t) cc_final: 0.7031 (t) REVERT: e 98 CYS cc_start: 0.5050 (p) cc_final: 0.4277 (p) REVERT: e 115 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7532 (ttm-80) REVERT: f 46 ILE cc_start: 0.8242 (mm) cc_final: 0.7997 (mm) REVERT: f 106 GLU cc_start: 0.7791 (tt0) cc_final: 0.7521 (tt0) REVERT: f 115 ARG cc_start: 0.7647 (ttt180) cc_final: 0.6941 (tpt-90) REVERT: f 120 GLU cc_start: 0.8873 (tt0) cc_final: 0.8609 (tm-30) REVERT: f 124 GLU cc_start: 0.8365 (tt0) cc_final: 0.7996 (tp30) REVERT: f 128 MET cc_start: 0.5996 (mpp) cc_final: 0.5378 (mmt) REVERT: g 39 ASP cc_start: 0.9134 (p0) cc_final: 0.8820 (p0) REVERT: g 80 ASP cc_start: 0.8135 (t0) cc_final: 0.7918 (t0) REVERT: g 95 LYS cc_start: 0.8319 (mtpp) cc_final: 0.8109 (mtpp) REVERT: g 118 PHE cc_start: 0.8220 (t80) cc_final: 0.7863 (t80) REVERT: m 267 LEU cc_start: 0.7989 (tt) cc_final: 0.7694 (tp) REVERT: m 284 THR cc_start: 0.9050 (m) cc_final: 0.8816 (m) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1843 time to fit residues: 34.7334 Evaluate side-chains 126 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 9.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.0270 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6352 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4724 Z= 0.178 Angle : 0.618 6.585 6404 Z= 0.315 Chirality : 0.043 0.322 751 Planarity : 0.005 0.069 785 Dihedral : 4.792 50.140 692 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.35), residues: 565 helix: 2.40 (0.33), residues: 220 sheet: -1.05 (0.62), residues: 83 loop : -2.68 (0.31), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP f 59 HIS 0.003 0.001 HIS f 61 PHE 0.011 0.001 PHE n 277 TYR 0.006 0.001 TYR f 113 ARG 0.011 0.001 ARG d 91 *********************** 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 145 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 45 GLU cc_start: 0.7163 (mp0) cc_final: 0.6910 (mp0) REVERT: d 68 ARG cc_start: 0.7532 (mtp180) cc_final: 0.7055 (mtp180) REVERT: d 70 ILE cc_start: 0.8214 (mt) cc_final: 0.7474 (tt) REVERT: d 71 TYR cc_start: 0.7171 (m-80) cc_final: 0.6912 (m-10) REVERT: e 49 CYS cc_start: 0.7560 (t) cc_final: 0.7019 (t) REVERT: e 98 CYS cc_start: 0.4976 (p) cc_final: 0.4287 (p) REVERT: e 115 ARG cc_start: 0.7759 (ttm-80) cc_final: 0.7536 (ttm-80) REVERT: f 46 ILE cc_start: 0.8231 (mm) cc_final: 0.7992 (mm) REVERT: f 106 GLU cc_start: 0.7846 (tt0) cc_final: 0.7516 (tt0) REVERT: f 115 ARG cc_start: 0.7536 (ttt180) cc_final: 0.7098 (tpt-90) REVERT: f 120 GLU cc_start: 0.8971 (tt0) cc_final: 0.8640 (tm-30) REVERT: f 124 GLU cc_start: 0.8400 (tt0) cc_final: 0.7989 (tp30) REVERT: f 128 MET cc_start: 0.5945 (mpp) cc_final: 0.5320 (mmt) REVERT: g 34 TYR cc_start: 0.7705 (t80) cc_final: 0.7486 (t80) REVERT: g 39 ASP cc_start: 0.8991 (p0) cc_final: 0.8697 (p0) REVERT: g 80 ASP cc_start: 0.8148 (t0) cc_final: 0.7089 (t0) REVERT: g 82 ARG cc_start: 0.8592 (ptp-170) cc_final: 0.8069 (ptp-170) REVERT: g 118 PHE cc_start: 0.8227 (t80) cc_final: 0.7909 (t80) REVERT: g 139 GLN cc_start: 0.8470 (pp30) cc_final: 0.8226 (pp30) REVERT: m 284 THR cc_start: 0.9056 (m) cc_final: 0.8797 (m) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1659 time to fit residues: 30.0777 Evaluate side-chains 124 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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: 3.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6498 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4724 Z= 0.296 Angle : 0.748 10.323 6404 Z= 0.379 Chirality : 0.046 0.185 751 Planarity : 0.004 0.041 785 Dihedral : 5.206 45.232 692 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: -0.90 (0.34), residues: 565 helix: 1.97 (0.32), residues: 221 sheet: -1.32 (0.55), residues: 101 loop : -2.87 (0.31), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP g 72 HIS 0.007 0.003 HIS d 89 PHE 0.015 0.002 PHE n 277 TYR 0.016 0.002 TYR f 111 ARG 0.007 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 146 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 24 ILE cc_start: 0.6474 (pt) cc_final: 0.6246 (pt) REVERT: d 70 ILE cc_start: 0.8421 (mt) cc_final: 0.8151 (mp) REVERT: d 71 TYR cc_start: 0.7237 (m-80) cc_final: 0.6917 (m-10) REVERT: d 98 GLU cc_start: 0.7824 (pt0) cc_final: 0.7220 (pm20) REVERT: e 49 CYS cc_start: 0.7297 (t) cc_final: 0.6493 (t) REVERT: e 98 CYS cc_start: 0.4791 (p) cc_final: 0.4303 (p) REVERT: f 46 ILE cc_start: 0.8223 (mm) cc_final: 0.8007 (mm) REVERT: f 89 GLU cc_start: 0.8059 (tt0) cc_final: 0.6782 (tt0) REVERT: f 106 GLU cc_start: 0.7862 (tt0) cc_final: 0.7431 (tt0) REVERT: f 115 ARG cc_start: 0.7766 (ttt180) cc_final: 0.6969 (tpt-90) REVERT: f 121 ASN cc_start: 0.7962 (m-40) cc_final: 0.7547 (m-40) REVERT: f 123 MET cc_start: 0.7949 (tmm) cc_final: 0.7739 (tmm) REVERT: f 124 GLU cc_start: 0.8512 (tt0) cc_final: 0.8133 (tp30) REVERT: f 128 MET cc_start: 0.6015 (mpp) cc_final: 0.5373 (mmt) REVERT: g 39 ASP cc_start: 0.8994 (p0) cc_final: 0.8631 (p0) REVERT: g 79 LYS cc_start: 0.8248 (mtpt) cc_final: 0.8014 (mtmt) REVERT: g 80 ASP cc_start: 0.8127 (t0) cc_final: 0.7307 (t0) REVERT: g 82 ARG cc_start: 0.8672 (ptp-170) cc_final: 0.8023 (ptp90) REVERT: g 118 PHE cc_start: 0.8259 (t80) cc_final: 0.7971 (t80) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1673 time to fit residues: 30.5519 Evaluate side-chains 122 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4724 Z= 0.230 Angle : 0.685 7.194 6404 Z= 0.349 Chirality : 0.045 0.167 751 Planarity : 0.004 0.042 785 Dihedral : 5.151 49.675 692 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % 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: -0.82 (0.34), residues: 565 helix: 2.10 (0.32), residues: 218 sheet: -1.46 (0.52), residues: 106 loop : -2.75 (0.32), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP f 59 HIS 0.004 0.001 HIS f 61 PHE 0.018 0.001 PHE b 40 TYR 0.009 0.001 TYR g 100 ARG 0.007 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 : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 70 ILE cc_start: 0.8384 (mt) cc_final: 0.7714 (tt) REVERT: d 71 TYR cc_start: 0.7054 (m-80) cc_final: 0.6753 (m-10) REVERT: d 87 GLN cc_start: 0.7338 (tm-30) cc_final: 0.7042 (tm-30) REVERT: d 98 GLU cc_start: 0.7773 (pt0) cc_final: 0.7280 (pm20) REVERT: e 36 TYR cc_start: 0.6969 (m-10) cc_final: 0.5764 (m-80) REVERT: e 49 CYS cc_start: 0.7473 (t) cc_final: 0.6149 (t) REVERT: e 98 CYS cc_start: 0.4801 (p) cc_final: 0.3699 (p) REVERT: f 86 GLU cc_start: 0.6225 (pt0) cc_final: 0.5987 (tm-30) REVERT: f 106 GLU cc_start: 0.7838 (tt0) cc_final: 0.7590 (tt0) REVERT: f 115 ARG cc_start: 0.7758 (ttt180) cc_final: 0.7020 (tpt-90) REVERT: f 121 ASN cc_start: 0.7844 (m-40) cc_final: 0.7404 (m-40) REVERT: f 124 GLU cc_start: 0.8451 (tt0) cc_final: 0.8163 (tp30) REVERT: f 128 MET cc_start: 0.6017 (mpp) cc_final: 0.5388 (mmt) REVERT: g 39 ASP cc_start: 0.8990 (p0) cc_final: 0.8646 (p0) REVERT: g 80 ASP cc_start: 0.8003 (t0) cc_final: 0.7195 (t0) REVERT: g 82 ARG cc_start: 0.8665 (ptp-170) cc_final: 0.7944 (ptp90) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1717 time to fit residues: 30.3930 Evaluate side-chains 128 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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: 5.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4724 Z= 0.235 Angle : 0.687 6.802 6404 Z= 0.352 Chirality : 0.045 0.166 751 Planarity : 0.004 0.043 785 Dihedral : 5.172 48.817 692 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -0.52 (0.35), residues: 565 helix: 2.32 (0.32), residues: 216 sheet: -1.20 (0.54), residues: 100 loop : -2.54 (0.32), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 72 HIS 0.004 0.001 HIS f 61 PHE 0.028 0.002 PHE g 118 TYR 0.013 0.001 TYR b 42 ARG 0.009 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 142 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 71 TYR cc_start: 0.6969 (m-80) cc_final: 0.6695 (m-80) REVERT: d 87 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7036 (tm-30) REVERT: d 96 CYS cc_start: 0.6385 (p) cc_final: 0.6147 (p) REVERT: d 98 GLU cc_start: 0.7823 (pt0) cc_final: 0.7250 (pm20) REVERT: e 36 TYR cc_start: 0.7009 (m-10) cc_final: 0.5845 (m-80) REVERT: e 49 CYS cc_start: 0.7421 (t) cc_final: 0.6023 (t) REVERT: e 98 CYS cc_start: 0.4796 (p) cc_final: 0.3648 (p) REVERT: e 124 GLU cc_start: 0.8211 (tp30) cc_final: 0.7867 (tp30) REVERT: f 46 ILE cc_start: 0.8158 (mm) cc_final: 0.7897 (mm) REVERT: f 81 HIS cc_start: 0.6424 (t-170) cc_final: 0.6194 (t70) REVERT: f 86 GLU cc_start: 0.6365 (pt0) cc_final: 0.6072 (tm-30) REVERT: f 89 GLU cc_start: 0.8008 (tt0) cc_final: 0.7795 (tt0) REVERT: f 101 ARG cc_start: 0.7452 (mtp85) cc_final: 0.6855 (tpp-160) REVERT: f 106 GLU cc_start: 0.7900 (tt0) cc_final: 0.7648 (tt0) REVERT: f 115 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7180 (tpt-90) REVERT: f 124 GLU cc_start: 0.8479 (tt0) cc_final: 0.8167 (tp30) REVERT: f 128 MET cc_start: 0.5994 (mpp) cc_final: 0.5343 (mmt) REVERT: g 39 ASP cc_start: 0.8971 (p0) cc_final: 0.8767 (p0) REVERT: g 80 ASP cc_start: 0.8030 (t0) cc_final: 0.7230 (t0) REVERT: g 82 ARG cc_start: 0.8559 (ptp-170) cc_final: 0.7784 (ptp90) REVERT: g 111 ASN cc_start: 0.7665 (m110) cc_final: 0.6893 (p0) REVERT: m 267 LEU cc_start: 0.7969 (tt) cc_final: 0.7719 (tp) REVERT: m 284 THR cc_start: 0.8968 (m) cc_final: 0.8706 (m) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1683 time to fit residues: 30.4929 Evaluate side-chains 126 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6466 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4724 Z= 0.260 Angle : 0.727 7.611 6404 Z= 0.369 Chirality : 0.046 0.178 751 Planarity : 0.004 0.042 785 Dihedral : 5.300 48.043 692 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % 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: -0.64 (0.34), residues: 565 helix: 2.10 (0.32), residues: 216 sheet: -1.07 (0.58), residues: 90 loop : -2.54 (0.32), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 72 HIS 0.004 0.001 HIS f 61 PHE 0.017 0.002 PHE b 40 TYR 0.011 0.001 TYR a 33 ARG 0.009 0.001 ARG f 101 ********************** 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 140 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 59 ASP cc_start: 0.8768 (p0) cc_final: 0.8557 (p0) REVERT: d 96 CYS cc_start: 0.6378 (p) cc_final: 0.5887 (p) REVERT: e 36 TYR cc_start: 0.6999 (m-10) cc_final: 0.5877 (m-80) REVERT: e 49 CYS cc_start: 0.7313 (t) cc_final: 0.5789 (t) REVERT: e 91 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7430 (tm-30) REVERT: e 98 CYS cc_start: 0.4554 (p) cc_final: 0.3386 (p) REVERT: e 124 GLU cc_start: 0.8186 (tp30) cc_final: 0.7860 (tp30) REVERT: f 46 ILE cc_start: 0.8162 (mm) cc_final: 0.7921 (mm) REVERT: f 81 HIS cc_start: 0.6388 (t-170) cc_final: 0.6141 (t70) REVERT: f 86 GLU cc_start: 0.6438 (pt0) cc_final: 0.6071 (tm-30) REVERT: f 106 GLU cc_start: 0.7902 (tt0) cc_final: 0.7486 (tt0) REVERT: f 115 ARG cc_start: 0.7799 (ttt180) cc_final: 0.7162 (tpt-90) REVERT: f 124 GLU cc_start: 0.8474 (tt0) cc_final: 0.8142 (tp30) REVERT: f 128 MET cc_start: 0.5999 (mpp) cc_final: 0.5357 (mmt) REVERT: g 77 ASN cc_start: 0.8625 (p0) cc_final: 0.8305 (p0) REVERT: g 79 LYS cc_start: 0.8276 (mtpt) cc_final: 0.8008 (mtmt) REVERT: g 80 ASP cc_start: 0.8021 (t0) cc_final: 0.7243 (t0) REVERT: g 82 ARG cc_start: 0.8556 (ptp-170) cc_final: 0.7802 (ptp90) REVERT: g 95 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7742 (ttmt) REVERT: g 111 ASN cc_start: 0.7839 (m110) cc_final: 0.6911 (p0) REVERT: g 118 PHE cc_start: 0.8144 (t80) cc_final: 0.7701 (t80) REVERT: m 267 LEU cc_start: 0.8013 (tt) cc_final: 0.7799 (tp) REVERT: m 284 THR cc_start: 0.9023 (m) cc_final: 0.8748 (m) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1586 time to fit residues: 27.8860 Evaluate side-chains 122 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.164628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144570 restraints weight = 7860.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144474 restraints weight = 10661.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145081 restraints weight = 9898.764| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4724 Z= 0.238 Angle : 0.723 9.339 6404 Z= 0.367 Chirality : 0.045 0.175 751 Planarity : 0.004 0.042 785 Dihedral : 5.275 48.891 692 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.63 (0.34), residues: 565 helix: 2.07 (0.32), residues: 216 sheet: -0.92 (0.58), residues: 88 loop : -2.55 (0.32), residues: 261 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 0.018 0.002 PHE b 40 TYR 0.009 0.001 TYR d 79 ARG 0.003 0.001 ARG e 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1455.58 seconds wall clock time: 26 minutes 30.47 seconds (1590.47 seconds total)