Starting phenix.real_space_refine on Thu Mar 14 23:04:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7v_15903/03_2024/8b7v_15903.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7v_15903/03_2024/8b7v_15903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7v_15903/03_2024/8b7v_15903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7v_15903/03_2024/8b7v_15903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7v_15903/03_2024/8b7v_15903.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7v_15903/03_2024/8b7v_15903.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 42 5.16 5 C 6330 2.51 5 N 1713 2.21 5 O 1965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ASP 133": "OD1" <-> "OD2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "B ASP 2": "OD1" <-> "OD2" Residue "B TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B ASP 55": "OD1" <-> "OD2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B ASP 282": "OD1" <-> "OD2" Residue "B ASP 285": "OD1" <-> "OD2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 355": "OD1" <-> "OD2" Residue "B TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B ASP 409": "OD1" <-> "OD2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C ASP 73": "OD1" <-> "OD2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C ASP 192": "OD1" <-> "OD2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C ASP 300": "OD1" <-> "OD2" Residue "C TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 397": "OD1" <-> "OD2" Residue "C PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10050 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3350 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412} Chain: "B" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3350 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412} Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3350 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412} Time building chain proxies: 5.56, per 1000 atoms: 0.55 Number of scatterers: 10050 At special positions: 0 Unit cell: (97.11, 96.28, 76.36, 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 42 16.00 O 1965 8.00 N 1713 7.00 C 6330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 38 " distance=2.03 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: 3.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 12 sheets defined 4.0% alpha, 57.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'B' and resid 113 through 116 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'C' and resid 113 through 116 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.566A pdb=" N ASP C 162 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 397 through 401 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 14 removed outlier: 4.015A pdb=" N LEU A 46 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 62 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE A 58 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS A 52 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA A 65 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N PHE A 81 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU A 139 " --> pdb=" O ASN A 131 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 142 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY A 150 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASN A 165 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 168 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 178 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU A 187 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU A 180 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY A 185 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP A 213 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112 removed outlier: 3.516A pdb=" N TRP A 120 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 112 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR A 118 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 14 removed outlier: 3.968A pdb=" N LEU B 46 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 62 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE B 58 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS B 52 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LYS B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA B 65 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N PHE B 81 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 11.618A pdb=" N GLY B 124 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N SER B 147 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY B 126 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ARG B 145 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLY B 128 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA B 143 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU B 130 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 141 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 142 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY B 150 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN B 165 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 168 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU B 187 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP B 213 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N MET B 320 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 112 removed outlier: 6.898A pdb=" N HIS B 110 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 378 Processing sheet with id=AA9, first strand: chain 'C' and resid 203 through 204 removed outlier: 4.081A pdb=" N ALA C 142 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY C 150 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN C 165 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA C 168 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU C 187 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU C 180 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLY C 185 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TRP C 213 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP C 284 " --> pdb=" O MET C 280 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N MET C 320 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 46 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 62 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE C 58 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS C 52 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER C 57 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY C 88 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR C 59 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL C 86 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP C 61 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 84 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASN C 63 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU C 139 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.659A pdb=" N VAL C 112 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N TYR C 118 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 252 through 254 Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.020A pdb=" N LYS C 392 " --> pdb=" O ASP C 379 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1551 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: 3.32 Time building geometry restraints manager: 4.07 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: 2204 1.34 - 1.46: 3960 1.46 - 1.58: 4087 1.58 - 1.71: 0 1.71 - 1.83: 78 Bond restraints: 10329 Sorted by residual: bond pdb=" CD ARG B 335 " pdb=" NE ARG B 335 " ideal model delta sigma weight residual 1.458 1.510 -0.052 1.40e-02 5.10e+03 1.39e+01 bond pdb=" CD ARG C 335 " pdb=" NE ARG C 335 " ideal model delta sigma weight residual 1.458 1.510 -0.052 1.40e-02 5.10e+03 1.36e+01 bond pdb=" CD ARG A 335 " pdb=" NE ARG A 335 " ideal model delta sigma weight residual 1.458 1.509 -0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" CE1 HIS B 275 " pdb=" NE2 HIS B 275 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.30e+01 bond pdb=" CE1 HIS C 275 " pdb=" NE2 HIS C 275 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.27e+01 ... (remaining 10324 not shown) Histogram of bond angle deviations from ideal: 94.28 - 102.10: 36 102.10 - 109.91: 2060 109.91 - 117.73: 5009 117.73 - 125.54: 6594 125.54 - 133.36: 311 Bond angle restraints: 14010 Sorted by residual: angle pdb=" CA ARG C 360 " pdb=" C ARG C 360 " pdb=" N PRO C 361 " ideal model delta sigma weight residual 117.68 126.03 -8.35 7.10e-01 1.98e+00 1.38e+02 angle pdb=" CA THR B 317 " pdb=" C THR B 317 " pdb=" N PRO B 318 " ideal model delta sigma weight residual 117.96 125.95 -7.99 8.10e-01 1.52e+00 9.72e+01 angle pdb=" CA THR C 317 " pdb=" C THR C 317 " pdb=" N PRO C 318 " ideal model delta sigma weight residual 117.96 125.52 -7.56 8.10e-01 1.52e+00 8.71e+01 angle pdb=" CA ARG B 360 " pdb=" C ARG B 360 " pdb=" N PRO B 361 " ideal model delta sigma weight residual 117.95 125.05 -7.10 7.70e-01 1.69e+00 8.50e+01 angle pdb=" CA ASP A 211 " pdb=" CB ASP A 211 " pdb=" CG ASP A 211 " ideal model delta sigma weight residual 112.60 119.94 -7.34 1.00e+00 1.00e+00 5.39e+01 ... (remaining 14005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.77: 5385 18.77 - 37.54: 313 37.54 - 56.32: 60 56.32 - 75.09: 58 75.09 - 93.86: 22 Dihedral angle restraints: 5838 sinusoidal: 2274 harmonic: 3564 Sorted by residual: dihedral pdb=" N GLN B 70 " pdb=" C GLN B 70 " pdb=" CA GLN B 70 " pdb=" CB GLN B 70 " ideal model delta harmonic sigma weight residual 122.80 137.61 -14.81 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" CA TYR B 32 " pdb=" C TYR B 32 " pdb=" N ARG B 33 " pdb=" CA ARG B 33 " ideal model delta harmonic sigma weight residual -180.00 -150.66 -29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" C GLN B 70 " pdb=" N GLN B 70 " pdb=" CA GLN B 70 " pdb=" CB GLN B 70 " ideal model delta harmonic sigma weight residual -122.60 -137.11 14.51 0 2.50e+00 1.60e-01 3.37e+01 ... (remaining 5835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1021 0.116 - 0.232: 284 0.232 - 0.348: 53 0.348 - 0.464: 7 0.464 - 0.580: 3 Chirality restraints: 1368 Sorted by residual: chirality pdb=" CA GLN B 70 " pdb=" N GLN B 70 " pdb=" C GLN B 70 " pdb=" CB GLN B 70 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" CA GLN A 70 " pdb=" N GLN A 70 " pdb=" C GLN A 70 " pdb=" CB GLN A 70 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA GLN C 70 " pdb=" N GLN C 70 " pdb=" C GLN C 70 " pdb=" CB GLN C 70 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.84e+00 ... (remaining 1365 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 118 " -0.202 2.00e-02 2.50e+03 1.21e-01 2.91e+02 pdb=" CG TYR C 118 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR C 118 " 0.078 2.00e-02 2.50e+03 pdb=" CD2 TYR C 118 " 0.087 2.00e-02 2.50e+03 pdb=" CE1 TYR C 118 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 TYR C 118 " 0.089 2.00e-02 2.50e+03 pdb=" CZ TYR C 118 " 0.043 2.00e-02 2.50e+03 pdb=" OH TYR C 118 " -0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 118 " -0.164 2.00e-02 2.50e+03 9.65e-02 1.86e+02 pdb=" CG TYR A 118 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 118 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 118 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 118 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 TYR A 118 " 0.060 2.00e-02 2.50e+03 pdb=" CZ TYR A 118 " 0.036 2.00e-02 2.50e+03 pdb=" OH TYR A 118 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 32 " 0.125 2.00e-02 2.50e+03 7.29e-02 1.06e+02 pdb=" CG TYR A 32 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 32 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR A 32 " -0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR A 32 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 32 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR A 32 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 32 " 0.124 2.00e-02 2.50e+03 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3752 2.91 - 3.41: 8290 3.41 - 3.90: 17791 3.90 - 4.40: 19949 4.40 - 4.90: 35305 Nonbonded interactions: 85087 Sorted by model distance: nonbonded pdb=" N THR B 317 " pdb=" O THR B 317 " model vdw 2.409 2.496 nonbonded pdb=" N THR C 317 " pdb=" O THR C 317 " model vdw 2.425 2.496 nonbonded pdb=" N ARG C 360 " pdb=" O ARG C 360 " model vdw 2.449 2.496 nonbonded pdb=" N THR A 317 " pdb=" O THR A 317 " model vdw 2.465 2.496 nonbonded pdb=" N ARG B 360 " pdb=" O ARG B 360 " model vdw 2.488 2.496 ... (remaining 85082 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: 0.010 Normalize map: mean=0, sd=1: 0.130 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: 1.140 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.420 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.015 0.052 10329 Z= 0.958 Angle : 1.804 10.461 14010 Z= 1.245 Chirality : 0.114 0.580 1368 Planarity : 0.019 0.276 1854 Dihedral : 15.921 93.858 3591 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 0.05 Ramachandran Plot: Outliers : 0.64 % Allowed : 2.63 % Favored : 96.74 % Rotamer: Outliers : 1.76 % Allowed : 5.29 % Favored : 92.94 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 12.50 % 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: -0.16 (0.21), residues: 1257 helix: -4.93 (0.16), residues: 18 sheet: 1.57 (0.19), residues: 612 loop : -1.85 (0.20), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.015 TRP A 51 HIS 0.012 0.003 HIS A 4 PHE 0.076 0.011 PHE C 254 TYR 0.211 0.022 TYR C 118 ARG 0.042 0.005 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.090 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 146 average time/residue: 1.4998 time to fit residues: 232.2376 Evaluate side-chains 76 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain B residue 420 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS A 70 GLN A 201 ASN A 349 GLN B 70 GLN B 90 ASN B 201 ASN C 4 HIS C 70 GLN C 159 ASN C 165 ASN C 201 ASN C 264 ASN C 266 ASN C 341 ASN C 386 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10329 Z= 0.209 Angle : 0.609 5.625 14010 Z= 0.350 Chirality : 0.046 0.156 1368 Planarity : 0.004 0.063 1854 Dihedral : 6.212 59.533 1381 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.43 % Favored : 98.41 % Rotamer: Outliers : 2.94 % Allowed : 8.43 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.17 (0.21), residues: 1257 helix: -4.93 (0.14), residues: 18 sheet: 1.30 (0.19), residues: 618 loop : -1.56 (0.21), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 420 HIS 0.004 0.001 HIS C 113 PHE 0.012 0.001 PHE B 23 TYR 0.015 0.001 TYR C 343 ARG 0.009 0.001 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 79 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 116 ASP cc_start: 0.6111 (t0) cc_final: 0.5911 (t0) outliers start: 30 outliers final: 2 residues processed: 98 average time/residue: 1.3307 time to fit residues: 139.9358 Evaluate side-chains 64 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain C residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10329 Z= 0.283 Angle : 0.594 8.409 14010 Z= 0.331 Chirality : 0.044 0.154 1368 Planarity : 0.004 0.062 1854 Dihedral : 5.527 27.966 1377 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.07 % Favored : 97.85 % Rotamer: Outliers : 2.06 % Allowed : 9.71 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.31 (0.21), residues: 1257 helix: -5.01 (0.12), residues: 18 sheet: 1.12 (0.20), residues: 594 loop : -1.44 (0.20), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 51 HIS 0.004 0.001 HIS A 113 PHE 0.009 0.001 PHE A 58 TYR 0.015 0.001 TYR A 343 ARG 0.005 0.001 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 90 average time/residue: 1.4119 time to fit residues: 136.2923 Evaluate side-chains 61 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 30.0000 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 109 optimal weight: 0.3980 chunk 32 optimal weight: 9.9990 overall best weight: 6.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN B 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10329 Z= 0.274 Angle : 0.564 7.190 14010 Z= 0.316 Chirality : 0.043 0.146 1368 Planarity : 0.004 0.062 1854 Dihedral : 5.323 25.104 1377 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.15 % Favored : 97.77 % Rotamer: Outliers : 1.37 % Allowed : 11.67 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1257 helix: -5.02 (0.12), residues: 18 sheet: 1.04 (0.20), residues: 597 loop : -1.43 (0.20), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 420 HIS 0.003 0.001 HIS B 113 PHE 0.008 0.001 PHE B 23 TYR 0.014 0.001 TYR A 343 ARG 0.006 0.001 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 1.212 Fit side-chains outliers start: 14 outliers final: 2 residues processed: 74 average time/residue: 1.4701 time to fit residues: 116.4152 Evaluate side-chains 57 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain C residue 38 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.7136 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10329 Z= 0.218 Angle : 0.548 8.568 14010 Z= 0.306 Chirality : 0.043 0.139 1368 Planarity : 0.004 0.062 1854 Dihedral : 5.197 25.335 1377 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.15 % Favored : 97.77 % Rotamer: Outliers : 1.08 % Allowed : 12.35 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1257 helix: -5.02 (0.11), residues: 18 sheet: 0.92 (0.20), residues: 597 loop : -1.40 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 51 HIS 0.002 0.001 HIS A 113 PHE 0.006 0.001 PHE A 58 TYR 0.013 0.001 TYR A 343 ARG 0.005 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 1.188 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 70 average time/residue: 1.4513 time to fit residues: 109.1586 Evaluate side-chains 61 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain B residue 147 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 30.0000 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 121 optimal weight: 30.0000 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 overall best weight: 12.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 228 ASN B 349 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 10329 Z= 0.506 Angle : 0.642 6.482 14010 Z= 0.357 Chirality : 0.045 0.149 1368 Planarity : 0.004 0.059 1854 Dihedral : 5.428 23.908 1377 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 1.47 % Allowed : 13.04 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1257 helix: -5.07 (0.12), residues: 18 sheet: 0.67 (0.20), residues: 642 loop : -1.63 (0.21), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 51 HIS 0.005 0.001 HIS B 113 PHE 0.010 0.001 PHE C 398 TYR 0.018 0.001 TYR A 343 ARG 0.004 0.001 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 1.049 Fit side-chains REVERT: C 239 MET cc_start: 0.7027 (mmt) cc_final: 0.6818 (mmp) outliers start: 15 outliers final: 2 residues processed: 68 average time/residue: 1.3292 time to fit residues: 97.4947 Evaluate side-chains 60 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 147 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.7178 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10329 Z= 0.287 Angle : 0.577 7.278 14010 Z= 0.321 Chirality : 0.043 0.141 1368 Planarity : 0.004 0.060 1854 Dihedral : 5.253 27.905 1377 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.39 % Favored : 97.45 % Rotamer: Outliers : 0.69 % Allowed : 13.14 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.22), residues: 1257 helix: -5.06 (0.11), residues: 18 sheet: 0.77 (0.20), residues: 600 loop : -1.52 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 94 HIS 0.002 0.001 HIS C 113 PHE 0.006 0.001 PHE A 58 TYR 0.034 0.001 TYR B 32 ARG 0.004 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.084 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 1.4245 time to fit residues: 96.4743 Evaluate side-chains 57 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 147 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.7172 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10329 Z= 0.276 Angle : 0.564 7.022 14010 Z= 0.315 Chirality : 0.043 0.137 1368 Planarity : 0.004 0.059 1854 Dihedral : 5.171 25.578 1377 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.39 % Favored : 97.53 % Rotamer: Outliers : 0.88 % Allowed : 13.53 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.22), residues: 1257 helix: -5.06 (0.11), residues: 18 sheet: 0.62 (0.21), residues: 582 loop : -1.40 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.003 0.001 HIS C 113 PHE 0.005 0.001 PHE A 254 TYR 0.028 0.001 TYR B 32 ARG 0.004 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 1.143 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 1.4653 time to fit residues: 99.3082 Evaluate side-chains 59 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain C residue 417 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 119 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.7170 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10329 Z= 0.271 Angle : 0.574 6.904 14010 Z= 0.319 Chirality : 0.043 0.137 1368 Planarity : 0.004 0.059 1854 Dihedral : 5.124 24.317 1377 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.31 % Favored : 97.61 % Rotamer: Outliers : 0.78 % Allowed : 13.92 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.62 (0.22), residues: 1257 helix: -5.06 (0.11), residues: 18 sheet: 0.67 (0.20), residues: 588 loop : -1.36 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 94 HIS 0.002 0.001 HIS C 113 PHE 0.005 0.001 PHE A 254 TYR 0.027 0.001 TYR B 32 ARG 0.004 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 1.237 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 1.4545 time to fit residues: 98.4975 Evaluate side-chains 57 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain C residue 417 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 106 optimal weight: 0.4980 overall best weight: 4.4988 ------------------------------------------------------------------------------- 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: 0.7148 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10329 Z= 0.211 Angle : 0.551 6.861 14010 Z= 0.306 Chirality : 0.042 0.138 1368 Planarity : 0.004 0.057 1854 Dihedral : 5.014 24.144 1377 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.23 % Favored : 97.69 % Rotamer: Outliers : 0.59 % Allowed : 14.31 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1257 helix: -5.05 (0.11), residues: 18 sheet: 0.68 (0.20), residues: 591 loop : -1.29 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 94 HIS 0.002 0.000 HIS A 275 PHE 0.004 0.001 PHE A 58 TYR 0.024 0.001 TYR B 32 ARG 0.004 0.000 ARG B 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 1.105 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 1.4244 time to fit residues: 91.8040 Evaluate side-chains 61 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 417 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.067632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.054911 restraints weight = 20724.689| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.11 r_work: 0.2546 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10329 Z= 0.248 Angle : 0.575 6.935 14010 Z= 0.317 Chirality : 0.043 0.139 1368 Planarity : 0.004 0.055 1854 Dihedral : 5.020 24.082 1377 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.07 % Favored : 97.85 % Rotamer: Outliers : 0.59 % Allowed : 14.31 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.61 (0.22), residues: 1257 helix: -5.05 (0.11), residues: 18 sheet: 0.64 (0.21), residues: 585 loop : -1.29 (0.21), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 94 HIS 0.002 0.001 HIS C 113 PHE 0.005 0.001 PHE C 254 TYR 0.024 0.001 TYR B 32 ARG 0.004 0.000 ARG B 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2562.92 seconds wall clock time: 46 minutes 35.13 seconds (2795.13 seconds total)