Starting phenix.real_space_refine on Sun Mar 10 22:07:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/03_2024/8a01_15044.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/03_2024/8a01_15044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/03_2024/8a01_15044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/03_2024/8a01_15044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/03_2024/8a01_15044.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a01_15044/03_2024/8a01_15044.pdb" } resolution = 3.2 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= 0.016 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 15 5.16 5 C 3495 2.51 5 N 885 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 29": "OD1" <-> "OD2" Residue "C ASP 108": "OD1" <-> "OD2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "B" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "A" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Time building chain proxies: 3.50, per 1000 atoms: 0.64 Number of scatterers: 5511 At special positions: 0 Unit cell: (104.16, 97.96, 71.92, 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 15 16.00 O 1116 8.00 N 885 7.00 C 3495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 1.0 seconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 17 sheets defined 10.2% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 60 through 68 removed outlier: 3.514A pdb=" N SER C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 187 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.652A pdb=" N LEU B 35 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 removed outlier: 3.638A pdb=" N SER B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'A' and resid 31 through 35 removed outlier: 3.617A pdb=" N LEU A 35 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 178 through 188 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 7 removed outlier: 5.422A pdb=" N LYS C 2 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY C 119 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 23 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 17 removed outlier: 3.557A pdb=" N SER C 101 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE C 40 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN C 56 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 42 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 128 through 136 removed outlier: 5.664A pdb=" N ASN C 230 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 153 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 143 through 147 removed outlier: 6.570A pdb=" N GLN C 168 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 219 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER C 166 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE C 221 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP C 164 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS C 223 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 162 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 7 removed outlier: 6.711A pdb=" N LEU B 117 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR B 5 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR B 115 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ARG B 114 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N SER B 28 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP B 116 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU B 26 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N HIS B 118 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 24 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 120 " --> pdb=" O GLY B 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 17 removed outlier: 7.237A pdb=" N ILE B 40 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 56 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 42 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 5.260A pdb=" N SER B 93 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 137 removed outlier: 5.983A pdb=" N ASN B 230 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 157 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 153 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 143 through 146 removed outlier: 6.457A pdb=" N GLN B 168 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 219 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER B 166 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE B 221 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 164 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS B 223 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 162 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 194 through 195 Processing sheet with id=AB3, first strand: chain 'A' and resid 2 through 6 removed outlier: 5.584A pdb=" N LYS A 2 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY A 119 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 4 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 27 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 15 through 17 removed outlier: 7.006A pdb=" N ILE A 40 " --> pdb=" O ASN A 56 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN A 56 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 42 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 93 through 94 removed outlier: 5.757A pdb=" N SER A 93 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 128 through 137 removed outlier: 5.535A pdb=" N ASN A 230 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 153 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 143 through 147 removed outlier: 6.525A pdb=" N GLN A 168 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE A 219 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER A 166 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE A 221 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP A 164 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS A 223 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 162 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 194 through 195 201 hydrogen bonds defined for protein. 531 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: 1.34 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: 1.23 - 1.34: 1818 1.34 - 1.46: 1045 1.46 - 1.58: 2684 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5571 Sorted by residual: bond pdb=" CB ASN C 143 " pdb=" CG ASN C 143 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.18e-01 bond pdb=" CA ASN C 143 " pdb=" CB ASN C 143 " ideal model delta sigma weight residual 1.536 1.553 -0.017 2.08e-02 2.31e+03 6.77e-01 bond pdb=" CB ASP C 29 " pdb=" CG ASP C 29 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.77e-01 bond pdb=" CA ASN B 143 " pdb=" CB ASN B 143 " ideal model delta sigma weight residual 1.534 1.546 -0.012 1.76e-02 3.23e+03 4.52e-01 bond pdb=" CB ASN B 143 " pdb=" CG ASN B 143 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.19e-01 ... (remaining 5566 not shown) Histogram of bond angle deviations from ideal: 100.74 - 106.84: 70 106.84 - 112.94: 3152 112.94 - 119.04: 1509 119.04 - 125.14: 2796 125.14 - 131.24: 21 Bond angle restraints: 7548 Sorted by residual: angle pdb=" N LYS C 223 " pdb=" CA LYS C 223 " pdb=" C LYS C 223 " ideal model delta sigma weight residual 108.34 111.92 -3.58 1.31e+00 5.83e-01 7.46e+00 angle pdb=" C ALA C 138 " pdb=" N SER C 139 " pdb=" CA SER C 139 " ideal model delta sigma weight residual 121.54 125.84 -4.30 1.91e+00 2.74e-01 5.07e+00 angle pdb=" CA ASN C 143 " pdb=" CB ASN C 143 " pdb=" CG ASN C 143 " ideal model delta sigma weight residual 112.60 114.26 -1.66 1.00e+00 1.00e+00 2.75e+00 angle pdb=" C ILE C 3 " pdb=" N ALA C 4 " pdb=" CA ALA C 4 " ideal model delta sigma weight residual 121.62 118.94 2.68 1.83e+00 2.99e-01 2.14e+00 angle pdb=" CA TYR B 167 " pdb=" CB TYR B 167 " pdb=" CG TYR B 167 " ideal model delta sigma weight residual 113.90 116.48 -2.58 1.80e+00 3.09e-01 2.05e+00 ... (remaining 7543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3068 17.43 - 34.86: 270 34.86 - 52.29: 60 52.29 - 69.73: 13 69.73 - 87.16: 9 Dihedral angle restraints: 3420 sinusoidal: 1329 harmonic: 2091 Sorted by residual: dihedral pdb=" CB LYS A 57 " pdb=" CG LYS A 57 " pdb=" CD LYS A 57 " pdb=" CE LYS A 57 " ideal model delta sinusoidal sigma weight residual -180.00 -126.25 -53.75 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CB LYS B 200 " pdb=" CG LYS B 200 " pdb=" CD LYS B 200 " pdb=" CE LYS B 200 " ideal model delta sinusoidal sigma weight residual 60.00 112.52 -52.52 3 1.50e+01 4.44e-03 9.12e+00 dihedral pdb=" CB GLU B 141 " pdb=" CG GLU B 141 " pdb=" CD GLU B 141 " pdb=" OE1 GLU B 141 " ideal model delta sinusoidal sigma weight residual 0.00 80.58 -80.58 1 3.00e+01 1.11e-03 8.92e+00 ... (remaining 3417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 564 0.027 - 0.054: 188 0.054 - 0.081: 71 0.081 - 0.109: 72 0.109 - 0.136: 41 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE C 155 " pdb=" N ILE C 155 " pdb=" C ILE C 155 " pdb=" CB ILE C 155 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE C 42 " pdb=" N ILE C 42 " pdb=" C ILE C 42 " pdb=" CB ILE C 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE C 221 " pdb=" N ILE C 221 " pdb=" C ILE C 221 " pdb=" CB ILE C 221 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 933 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 178 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.03e-01 pdb=" N PRO B 179 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 178 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.03e-01 pdb=" N PRO C 179 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 211 " -0.013 5.00e-02 4.00e+02 2.04e-02 6.67e-01 pdb=" N PRO A 212 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.011 5.00e-02 4.00e+02 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1470 2.81 - 3.33: 4379 3.33 - 3.86: 8347 3.86 - 4.38: 9858 4.38 - 4.90: 18283 Nonbonded interactions: 42337 Sorted by model distance: nonbonded pdb=" OG SER C 163 " pdb=" O ASN C 222 " model vdw 2.289 2.440 nonbonded pdb=" O ILE A 64 " pdb=" OG1 THR A 68 " model vdw 2.297 2.440 nonbonded pdb=" NE2 GLN B 183 " pdb=" OD2 ASP A 77 " model vdw 2.328 2.520 nonbonded pdb=" OD1 ASN B 128 " pdb=" OG1 THR B 238 " model vdw 2.335 2.440 nonbonded pdb=" OD1 ASP C 98 " pdb=" N LYS C 99 " model vdw 2.375 2.520 ... (remaining 42332 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' selection = chain 'B' selection = chain 'C' } 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 individual isotropic 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: 0.340 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: 2.040 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.040 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.002 0.021 5571 Z= 0.118 Angle : 0.437 4.302 7548 Z= 0.240 Chirality : 0.046 0.136 936 Planarity : 0.002 0.024 960 Dihedral : 14.812 87.157 2064 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.02 (0.31), residues: 711 helix: 1.53 (0.67), residues: 63 sheet: 0.94 (0.31), residues: 282 loop : -1.06 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 118 PHE 0.006 0.001 PHE A 231 TYR 0.010 0.001 TYR C 43 ARG 0.001 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.620 Fit side-chains REVERT: C 171 ASN cc_start: 0.8580 (p0) cc_final: 0.8301 (p0) REVERT: A 149 GLN cc_start: 0.7674 (tt0) cc_final: 0.7446 (tt0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1714 time to fit residues: 26.6897 Evaluate side-chains 92 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN C 203 GLN B 149 GLN B 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.042 5571 Z= 0.582 Angle : 0.688 5.597 7548 Z= 0.364 Chirality : 0.054 0.159 936 Planarity : 0.004 0.029 960 Dihedral : 4.965 18.324 750 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.22 % Allowed : 9.52 % Favored : 88.25 % 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 (0.30), residues: 711 helix: 0.75 (0.65), residues: 63 sheet: 0.51 (0.31), residues: 291 loop : -1.29 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.012 0.002 PHE A 131 TYR 0.017 0.002 TYR C 43 ARG 0.003 0.001 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.670 Fit side-chains REVERT: A 149 GLN cc_start: 0.7935 (tt0) cc_final: 0.7735 (tt0) outliers start: 14 outliers final: 10 residues processed: 93 average time/residue: 0.1851 time to fit residues: 22.3807 Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5571 Z= 0.338 Angle : 0.537 4.334 7548 Z= 0.292 Chirality : 0.049 0.148 936 Planarity : 0.003 0.030 960 Dihedral : 4.647 16.315 750 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.90 % Allowed : 15.24 % Favored : 82.86 % 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 (0.30), residues: 711 helix: 0.83 (0.66), residues: 63 sheet: 0.47 (0.31), residues: 291 loop : -1.28 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 118 PHE 0.009 0.001 PHE B 231 TYR 0.014 0.001 TYR B 43 ARG 0.002 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.658 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 0.1745 time to fit residues: 20.8876 Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain A residue 7 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 37 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN C 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5571 Z= 0.181 Angle : 0.444 3.789 7548 Z= 0.247 Chirality : 0.047 0.141 936 Planarity : 0.003 0.030 960 Dihedral : 4.144 14.867 750 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.75 % Allowed : 16.83 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.31), residues: 711 helix: 1.17 (0.67), residues: 63 sheet: 0.54 (0.31), residues: 291 loop : -1.17 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 118 PHE 0.008 0.001 PHE C 231 TYR 0.013 0.001 TYR B 43 ARG 0.001 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.720 Fit side-chains REVERT: C 100 GLU cc_start: 0.7988 (mp0) cc_final: 0.7659 (mp0) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.1804 time to fit residues: 21.7292 Evaluate side-chains 85 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain A residue 7 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN A 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5571 Z= 0.195 Angle : 0.449 3.826 7548 Z= 0.249 Chirality : 0.047 0.141 936 Planarity : 0.003 0.028 960 Dihedral : 4.104 13.982 750 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.54 % Allowed : 17.14 % Favored : 80.32 % 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: -0.43 (0.31), residues: 711 helix: 1.27 (0.67), residues: 63 sheet: 0.39 (0.30), residues: 321 loop : -1.29 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 118 PHE 0.007 0.001 PHE C 231 TYR 0.013 0.001 TYR B 43 ARG 0.001 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.654 Fit side-chains REVERT: C 100 GLU cc_start: 0.7949 (mp0) cc_final: 0.7553 (mp0) REVERT: A 48 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8315 (m110) outliers start: 16 outliers final: 12 residues processed: 91 average time/residue: 0.1683 time to fit residues: 20.2434 Evaluate side-chains 92 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN B 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.048 5571 Z= 0.654 Angle : 0.717 6.017 7548 Z= 0.378 Chirality : 0.055 0.152 936 Planarity : 0.004 0.031 960 Dihedral : 5.136 19.563 750 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.02 % Allowed : 18.73 % Favored : 78.25 % 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: -0.88 (0.30), residues: 711 helix: 0.69 (0.66), residues: 63 sheet: 0.17 (0.30), residues: 291 loop : -1.50 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.013 0.003 PHE B 231 TYR 0.018 0.002 TYR B 43 ARG 0.003 0.001 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.629 Fit side-chains REVERT: A 48 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8543 (m110) outliers start: 19 outliers final: 16 residues processed: 91 average time/residue: 0.1720 time to fit residues: 20.6672 Evaluate side-chains 90 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 164 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5571 Z= 0.114 Angle : 0.421 3.752 7548 Z= 0.235 Chirality : 0.046 0.134 936 Planarity : 0.003 0.032 960 Dihedral : 4.025 13.305 750 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.90 % Allowed : 19.84 % Favored : 78.25 % 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: -0.46 (0.31), residues: 711 helix: 1.12 (0.67), residues: 63 sheet: 0.58 (0.31), residues: 276 loop : -1.29 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 118 PHE 0.008 0.001 PHE C 231 TYR 0.013 0.001 TYR B 43 ARG 0.002 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.687 Fit side-chains REVERT: C 141 GLU cc_start: 0.7932 (pt0) cc_final: 0.7685 (pt0) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.1777 time to fit residues: 21.2734 Evaluate side-chains 87 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5571 Z= 0.227 Angle : 0.471 3.886 7548 Z= 0.258 Chirality : 0.047 0.143 936 Planarity : 0.003 0.029 960 Dihedral : 4.189 14.989 750 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.90 % Allowed : 20.48 % Favored : 77.62 % 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: -0.42 (0.31), residues: 711 helix: 1.15 (0.68), residues: 63 sheet: 0.43 (0.31), residues: 291 loop : -1.16 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 118 PHE 0.007 0.001 PHE B 151 TYR 0.014 0.001 TYR B 43 ARG 0.001 0.000 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.645 Fit side-chains REVERT: C 141 GLU cc_start: 0.7966 (pt0) cc_final: 0.7723 (pt0) outliers start: 12 outliers final: 11 residues processed: 92 average time/residue: 0.1753 time to fit residues: 21.3543 Evaluate side-chains 90 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5571 Z= 0.192 Angle : 0.451 3.840 7548 Z= 0.249 Chirality : 0.047 0.140 936 Planarity : 0.003 0.029 960 Dihedral : 4.084 14.629 750 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.06 % Allowed : 20.16 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.31), residues: 711 helix: 1.19 (0.68), residues: 63 sheet: 0.45 (0.31), residues: 291 loop : -1.12 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 118 PHE 0.007 0.001 PHE C 231 TYR 0.013 0.001 TYR B 43 ARG 0.001 0.000 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.662 Fit side-chains REVERT: C 100 GLU cc_start: 0.7937 (mp0) cc_final: 0.7583 (mp0) REVERT: C 141 GLU cc_start: 0.7964 (pt0) cc_final: 0.7749 (pt0) REVERT: A 48 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8352 (m110) outliers start: 13 outliers final: 12 residues processed: 94 average time/residue: 0.1726 time to fit residues: 21.2754 Evaluate side-chains 92 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 5571 Z= 0.572 Angle : 0.667 5.353 7548 Z= 0.354 Chirality : 0.053 0.147 936 Planarity : 0.004 0.030 960 Dihedral : 4.961 18.983 750 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.38 % Allowed : 20.32 % Favored : 77.30 % 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: -0.71 (0.31), residues: 711 helix: 0.80 (0.67), residues: 63 sheet: 0.22 (0.31), residues: 288 loop : -1.29 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 118 PHE 0.011 0.002 PHE B 180 TYR 0.016 0.002 TYR B 43 ARG 0.003 0.001 ARG C 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.647 Fit side-chains REVERT: A 48 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8507 (m110) outliers start: 15 outliers final: 13 residues processed: 88 average time/residue: 0.1763 time to fit residues: 20.5472 Evaluate side-chains 86 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.111239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.099241 restraints weight = 7354.687| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.76 r_work: 0.2926 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5571 Z= 0.133 Angle : 0.428 3.797 7548 Z= 0.238 Chirality : 0.046 0.134 936 Planarity : 0.003 0.030 960 Dihedral : 4.057 13.595 750 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.90 % Allowed : 20.48 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.31), residues: 711 helix: 1.14 (0.68), residues: 63 sheet: 0.57 (0.32), residues: 276 loop : -1.27 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 118 PHE 0.007 0.001 PHE A 63 TYR 0.014 0.001 TYR B 43 ARG 0.001 0.000 ARG C 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1309.94 seconds wall clock time: 24 minutes 29.48 seconds (1469.48 seconds total)