Starting phenix.real_space_refine on Sat Mar 16 03:09:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vym_21464/03_2024/6vym_21464.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vym_21464/03_2024/6vym_21464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vym_21464/03_2024/6vym_21464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vym_21464/03_2024/6vym_21464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vym_21464/03_2024/6vym_21464.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vym_21464/03_2024/6vym_21464.pdb" } resolution = 3.7 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= -0.000 sd= 0.008 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 8715 2.51 5 N 2373 2.21 5 O 2443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 134": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "G GLU 134": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13573 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "B" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "C" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "D" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "E" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "F" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain: "G" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Time building chain proxies: 6.89, per 1000 atoms: 0.51 Number of scatterers: 13573 At special positions: 0 Unit cell: (100, 99, 111, 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 2443 8.00 N 2373 7.00 C 8715 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: 5.21 Conformation dependent library (CDL) restraints added in 2.5 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 53.5% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 28 through 60 Processing helix chain 'A' and resid 64 through 90 removed outlier: 3.643A pdb=" N PHE A 68 " --> pdb=" O THR A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 127 removed outlier: 4.037A pdb=" N VAL A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.586A pdb=" N ILE A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 245 through 264 removed outlier: 3.651A pdb=" N LEU A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 60 Processing helix chain 'B' and resid 64 through 90 removed outlier: 3.642A pdb=" N PHE B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 127 removed outlier: 4.036A pdb=" N VAL B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.586A pdb=" N ILE B 170 " --> pdb=" O PRO B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.651A pdb=" N LEU B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 60 Processing helix chain 'C' and resid 64 through 90 removed outlier: 3.642A pdb=" N PHE C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 127 removed outlier: 4.036A pdb=" N VAL C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.586A pdb=" N ILE C 170 " --> pdb=" O PRO C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 245 through 264 removed outlier: 3.652A pdb=" N LEU C 254 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 60 Processing helix chain 'D' and resid 64 through 90 removed outlier: 3.642A pdb=" N PHE D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 127 removed outlier: 4.036A pdb=" N VAL D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.586A pdb=" N ILE D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 245 through 264 removed outlier: 3.651A pdb=" N LEU D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 60 Processing helix chain 'E' and resid 64 through 90 removed outlier: 3.642A pdb=" N PHE E 68 " --> pdb=" O THR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 127 removed outlier: 4.036A pdb=" N VAL E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 3.585A pdb=" N ILE E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 245 through 264 removed outlier: 3.652A pdb=" N LEU E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 60 Processing helix chain 'F' and resid 64 through 90 removed outlier: 3.642A pdb=" N PHE F 68 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 127 removed outlier: 4.037A pdb=" N VAL F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.585A pdb=" N ILE F 170 " --> pdb=" O PRO F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 245 through 264 removed outlier: 3.651A pdb=" N LEU F 254 " --> pdb=" O TYR F 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 60 Processing helix chain 'G' and resid 64 through 90 removed outlier: 3.643A pdb=" N PHE G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 127 removed outlier: 4.035A pdb=" N VAL G 99 " --> pdb=" O SER G 95 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 123 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL G 125 " --> pdb=" O GLY G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 171 removed outlier: 3.585A pdb=" N ILE G 170 " --> pdb=" O PRO G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 212 Processing helix chain 'G' and resid 245 through 264 removed outlier: 3.651A pdb=" N LEU G 254 " --> pdb=" O TYR G 250 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 5.133A pdb=" N VAL A 145 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG A 156 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 164 " --> pdb=" O ILE G 175 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL G 145 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG G 156 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL F 145 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG F 156 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE F 162 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 164 " --> pdb=" O ILE E 175 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE E 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL E 145 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG E 156 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL D 145 " --> pdb=" O ARG D 156 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG D 156 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 162 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 164 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL C 145 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG C 156 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 162 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 164 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL B 145 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG B 156 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 162 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL B 164 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 175 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 7.286A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 276 removed outlier: 6.809A pdb=" N MET A 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 7.284A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 7.285A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 7.285A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 7.285A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 7.284A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 7.284A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 911 hydrogen bonds defined for protein. 2667 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: 4.24 Time building geometry restraints manager: 5.63 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: 4055 1.34 - 1.45: 1891 1.45 - 1.57: 7718 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 13748 Sorted by residual: bond pdb=" C ILE F 39 " pdb=" N VAL F 40 " ideal model delta sigma weight residual 1.335 1.426 -0.091 1.09e-02 8.42e+03 6.95e+01 bond pdb=" C VAL F 40 " pdb=" N GLY F 41 " ideal model delta sigma weight residual 1.335 1.284 0.051 1.19e-02 7.06e+03 1.83e+01 bond pdb=" C PHE E 268 " pdb=" N PRO E 269 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.20e-02 6.94e+03 2.62e+00 bond pdb=" C PHE D 268 " pdb=" N PRO D 269 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.20e-02 6.94e+03 2.57e+00 bond pdb=" C PHE B 268 " pdb=" N PRO B 269 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.20e-02 6.94e+03 2.46e+00 ... (remaining 13743 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.05: 287 107.05 - 113.78: 7931 113.78 - 120.51: 5641 120.51 - 127.24: 4719 127.24 - 133.97: 63 Bond angle restraints: 18641 Sorted by residual: angle pdb=" O ILE F 39 " pdb=" C ILE F 39 " pdb=" N VAL F 40 " ideal model delta sigma weight residual 121.87 126.84 -4.97 9.70e-01 1.06e+00 2.63e+01 angle pdb=" CA ILE F 39 " pdb=" C ILE F 39 " pdb=" N VAL F 40 " ideal model delta sigma weight residual 117.15 112.24 4.91 1.14e+00 7.69e-01 1.86e+01 angle pdb=" N GLY F 41 " pdb=" CA GLY F 41 " pdb=" C GLY F 41 " ideal model delta sigma weight residual 113.86 108.62 5.24 1.50e+00 4.44e-01 1.22e+01 angle pdb=" N ILE F 39 " pdb=" CA ILE F 39 " pdb=" C ILE F 39 " ideal model delta sigma weight residual 110.62 114.07 -3.45 1.02e+00 9.61e-01 1.14e+01 angle pdb=" C VAL F 40 " pdb=" N GLY F 41 " pdb=" CA GLY F 41 " ideal model delta sigma weight residual 120.34 124.58 -4.24 1.26e+00 6.30e-01 1.13e+01 ... (remaining 18636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.53: 6650 11.53 - 23.07: 1060 23.07 - 34.60: 396 34.60 - 46.13: 126 46.13 - 57.66: 28 Dihedral angle restraints: 8260 sinusoidal: 3171 harmonic: 5089 Sorted by residual: dihedral pdb=" CA PHE D 127 " pdb=" C PHE D 127 " pdb=" N ARG D 128 " pdb=" CA ARG D 128 " ideal model delta harmonic sigma weight residual 180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA PHE A 127 " pdb=" C PHE A 127 " pdb=" N ARG A 128 " pdb=" CA ARG A 128 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA PHE C 127 " pdb=" C PHE C 127 " pdb=" N ARG C 128 " pdb=" CA ARG C 128 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 8257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2011 0.086 - 0.171: 243 0.171 - 0.257: 17 0.257 - 0.343: 4 0.343 - 0.428: 7 Chirality restraints: 2282 Sorted by residual: chirality pdb=" CB ILE D 176 " pdb=" CA ILE D 176 " pdb=" CG1 ILE D 176 " pdb=" CG2 ILE D 176 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE E 176 " pdb=" CA ILE E 176 " pdb=" CG1 ILE E 176 " pdb=" CG2 ILE E 176 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CB ILE B 176 " pdb=" CA ILE B 176 " pdb=" CG1 ILE B 176 " pdb=" CG2 ILE B 176 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.57e+00 ... (remaining 2279 not shown) Planarity restraints: 2366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 40 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C VAL F 40 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL F 40 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY F 41 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 270 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO C 271 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 271 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 271 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 270 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO E 271 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 271 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 271 " 0.027 5.00e-02 4.00e+02 ... (remaining 2363 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4546 2.85 - 3.36: 13032 3.36 - 3.88: 22379 3.88 - 4.39: 24500 4.39 - 4.90: 43346 Nonbonded interactions: 107803 Sorted by model distance: nonbonded pdb=" O SER A 179 " pdb=" OG SER A 179 " model vdw 2.339 2.440 nonbonded pdb=" O SER G 179 " pdb=" OG SER G 179 " model vdw 2.339 2.440 nonbonded pdb=" O SER E 179 " pdb=" OG SER E 179 " model vdw 2.339 2.440 nonbonded pdb=" O SER B 179 " pdb=" OG SER B 179 " model vdw 2.339 2.440 nonbonded pdb=" O SER C 179 " pdb=" OG SER C 179 " model vdw 2.339 2.440 ... (remaining 107798 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 2.880 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 36.900 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.006 0.091 13748 Z= 0.423 Angle : 0.876 11.706 18641 Z= 0.484 Chirality : 0.059 0.428 2282 Planarity : 0.006 0.047 2366 Dihedral : 14.085 57.663 4984 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.15), residues: 1764 helix: -2.56 (0.12), residues: 896 sheet: -3.05 (0.31), residues: 189 loop : -3.48 (0.18), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 240 PHE 0.010 0.003 PHE B 130 TYR 0.008 0.001 TYR B 194 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 138 LEU cc_start: 0.8682 (mp) cc_final: 0.8465 (mp) REVERT: A 157 THR cc_start: 0.9412 (t) cc_final: 0.9146 (m) REVERT: A 161 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8934 (mtmm) REVERT: A 200 GLN cc_start: 0.8726 (tt0) cc_final: 0.8518 (tt0) REVERT: A 202 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8758 (mtpp) REVERT: A 273 MET cc_start: 0.8136 (ttm) cc_final: 0.7624 (ttm) REVERT: B 47 MET cc_start: 0.4077 (ttt) cc_final: 0.3650 (mtt) REVERT: B 111 LEU cc_start: 0.8787 (mp) cc_final: 0.8572 (mp) REVERT: B 157 THR cc_start: 0.9256 (t) cc_final: 0.8932 (m) REVERT: B 273 MET cc_start: 0.8068 (ttm) cc_final: 0.7540 (ttm) REVERT: C 47 MET cc_start: 0.4280 (ttt) cc_final: 0.3934 (mtt) REVERT: C 126 MET cc_start: 0.7484 (ttt) cc_final: 0.7194 (ttt) REVERT: C 151 PHE cc_start: 0.8789 (m-80) cc_final: 0.8583 (m-80) REVERT: C 200 GLN cc_start: 0.8681 (tt0) cc_final: 0.8372 (tt0) REVERT: C 273 MET cc_start: 0.8253 (ttm) cc_final: 0.8014 (ttm) REVERT: D 47 MET cc_start: 0.3559 (ttt) cc_final: 0.3088 (mtt) REVERT: D 157 THR cc_start: 0.8945 (t) cc_final: 0.8728 (m) REVERT: D 186 ASN cc_start: 0.8780 (m-40) cc_final: 0.8569 (m-40) REVERT: D 190 ILE cc_start: 0.9565 (mp) cc_final: 0.9331 (mt) REVERT: D 200 GLN cc_start: 0.8741 (tt0) cc_final: 0.8527 (tt0) REVERT: D 203 GLN cc_start: 0.8316 (tp40) cc_final: 0.8094 (tp40) REVERT: D 270 TYR cc_start: 0.9008 (m-80) cc_final: 0.8436 (m-80) REVERT: D 273 MET cc_start: 0.7905 (ttm) cc_final: 0.7662 (ttm) REVERT: E 47 MET cc_start: 0.3441 (ttt) cc_final: 0.3193 (ttt) REVERT: E 138 LEU cc_start: 0.8503 (mp) cc_final: 0.8239 (mp) REVERT: E 159 ASP cc_start: 0.8389 (p0) cc_final: 0.8126 (p0) REVERT: E 161 LYS cc_start: 0.9122 (mtmt) cc_final: 0.8842 (mtmm) REVERT: E 277 PHE cc_start: 0.7593 (m-10) cc_final: 0.7117 (m-10) REVERT: F 47 MET cc_start: 0.4310 (ttt) cc_final: 0.3874 (mtt) REVERT: F 115 LEU cc_start: 0.9121 (tt) cc_final: 0.8822 (tp) REVERT: F 190 ILE cc_start: 0.9619 (mp) cc_final: 0.9373 (mt) REVERT: F 200 GLN cc_start: 0.8926 (tt0) cc_final: 0.8671 (tt0) REVERT: F 272 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8507 (mm-40) REVERT: G 273 MET cc_start: 0.7991 (ttm) cc_final: 0.7313 (ttm) REVERT: G 274 ASP cc_start: 0.8146 (t0) cc_final: 0.7458 (t70) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.2476 time to fit residues: 147.7314 Evaluate side-chains 281 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 158 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 167 ASN B 167 ASN C 167 ASN D 167 ASN E 167 ASN F 167 ASN G 112 GLN G 167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13748 Z= 0.185 Angle : 0.573 8.327 18641 Z= 0.300 Chirality : 0.045 0.285 2282 Planarity : 0.004 0.033 2366 Dihedral : 5.262 23.314 1939 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.64 % Allowed : 17.82 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.17), residues: 1764 helix: -0.49 (0.16), residues: 903 sheet: -2.11 (0.29), residues: 238 loop : -3.22 (0.19), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP E 240 PHE 0.015 0.001 PHE E 178 TYR 0.007 0.001 TYR G 135 ARG 0.006 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 318 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 157 THR cc_start: 0.9376 (t) cc_final: 0.9169 (m) REVERT: A 161 LYS cc_start: 0.9184 (mtmt) cc_final: 0.8914 (mtmm) REVERT: A 209 ILE cc_start: 0.9090 (pt) cc_final: 0.8804 (mt) REVERT: A 273 MET cc_start: 0.8212 (ttm) cc_final: 0.7528 (ttm) REVERT: B 47 MET cc_start: 0.4004 (ttt) cc_final: 0.3552 (mtt) REVERT: B 273 MET cc_start: 0.8185 (ttm) cc_final: 0.7593 (ttm) REVERT: C 47 MET cc_start: 0.4625 (ttt) cc_final: 0.4320 (mtt) REVERT: C 126 MET cc_start: 0.7497 (ttt) cc_final: 0.7229 (ttt) REVERT: C 127 PHE cc_start: 0.6783 (t80) cc_final: 0.6462 (t80) REVERT: C 138 LEU cc_start: 0.8862 (mp) cc_final: 0.8498 (mp) REVERT: C 272 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8737 (mm-40) REVERT: C 273 MET cc_start: 0.8099 (ttm) cc_final: 0.7774 (ttm) REVERT: C 274 ASP cc_start: 0.8099 (t0) cc_final: 0.7670 (t70) REVERT: D 47 MET cc_start: 0.3611 (ttt) cc_final: 0.3120 (mtt) REVERT: D 127 PHE cc_start: 0.6827 (t80) cc_final: 0.6513 (t80) REVERT: D 203 GLN cc_start: 0.8462 (tp40) cc_final: 0.8124 (tp40) REVERT: D 270 TYR cc_start: 0.9076 (m-80) cc_final: 0.8642 (m-80) REVERT: D 272 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8692 (mm-40) REVERT: D 273 MET cc_start: 0.7659 (ttm) cc_final: 0.7302 (ttm) REVERT: E 47 MET cc_start: 0.3172 (ttt) cc_final: 0.2956 (ttt) REVERT: E 181 GLU cc_start: 0.8477 (tp30) cc_final: 0.8221 (tp30) REVERT: E 273 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7473 (mtm) REVERT: F 47 MET cc_start: 0.4504 (ttt) cc_final: 0.4103 (mtt) REVERT: F 115 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8659 (tt) REVERT: F 203 GLN cc_start: 0.8417 (tp40) cc_final: 0.8206 (tp40) REVERT: F 210 GLN cc_start: 0.8840 (tp40) cc_final: 0.8621 (mm110) REVERT: F 273 MET cc_start: 0.7979 (ttm) cc_final: 0.7318 (ttm) REVERT: G 273 MET cc_start: 0.7869 (ttm) cc_final: 0.7257 (ttm) REVERT: G 274 ASP cc_start: 0.8091 (t0) cc_final: 0.7720 (t70) outliers start: 38 outliers final: 16 residues processed: 340 average time/residue: 0.2072 time to fit residues: 107.8325 Evaluate side-chains 273 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 255 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 176 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 ASN G 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13748 Z= 0.403 Angle : 0.643 8.561 18641 Z= 0.338 Chirality : 0.047 0.407 2282 Planarity : 0.004 0.035 2366 Dihedral : 5.362 24.752 1939 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.72 % Allowed : 18.52 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.19), residues: 1764 helix: 0.44 (0.17), residues: 896 sheet: -2.04 (0.28), residues: 238 loop : -3.17 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 240 PHE 0.016 0.002 PHE E 178 TYR 0.010 0.001 TYR B 135 ARG 0.004 0.000 ARG G 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 254 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 186 ASN cc_start: 0.8881 (m-40) cc_final: 0.8644 (m-40) REVERT: A 273 MET cc_start: 0.8227 (ttm) cc_final: 0.7380 (ttm) REVERT: B 47 MET cc_start: 0.4204 (ttt) cc_final: 0.3794 (mtt) REVERT: B 273 MET cc_start: 0.8249 (ttm) cc_final: 0.7505 (ttm) REVERT: C 47 MET cc_start: 0.4503 (ttt) cc_final: 0.4253 (mtt) REVERT: C 115 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8907 (tp) REVERT: C 126 MET cc_start: 0.7787 (ttt) cc_final: 0.7495 (ttt) REVERT: C 127 PHE cc_start: 0.6973 (t80) cc_final: 0.6542 (t80) REVERT: C 272 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8689 (mm-40) REVERT: C 273 MET cc_start: 0.8091 (ttm) cc_final: 0.7781 (ttm) REVERT: D 47 MET cc_start: 0.3648 (ttt) cc_final: 0.3170 (mtt) REVERT: D 203 GLN cc_start: 0.8547 (tp40) cc_final: 0.8268 (tp40) REVERT: D 270 TYR cc_start: 0.9126 (m-80) cc_final: 0.8711 (m-80) REVERT: D 273 MET cc_start: 0.7718 (ttm) cc_final: 0.7379 (ttm) REVERT: E 47 MET cc_start: 0.3327 (ttt) cc_final: 0.3115 (ttt) REVERT: E 126 MET cc_start: 0.7872 (ttt) cc_final: 0.7657 (ttt) REVERT: E 181 GLU cc_start: 0.8532 (tp30) cc_final: 0.8304 (tp30) REVERT: E 273 MET cc_start: 0.8019 (mtm) cc_final: 0.7681 (mtm) REVERT: F 47 MET cc_start: 0.4581 (ttt) cc_final: 0.4239 (ttt) REVERT: F 115 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8905 (tt) REVERT: F 272 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8663 (mm110) REVERT: G 274 ASP cc_start: 0.8082 (t0) cc_final: 0.7758 (t70) outliers start: 68 outliers final: 38 residues processed: 314 average time/residue: 0.1993 time to fit residues: 97.7114 Evaluate side-chains 271 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 231 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 106 optimal weight: 50.0000 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13748 Z= 0.287 Angle : 0.588 8.152 18641 Z= 0.307 Chirality : 0.046 0.381 2282 Planarity : 0.003 0.034 2366 Dihedral : 5.077 23.918 1939 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.92 % Allowed : 18.93 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.19), residues: 1764 helix: 0.78 (0.17), residues: 896 sheet: -1.83 (0.30), residues: 224 loop : -3.00 (0.20), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 240 PHE 0.018 0.001 PHE D 277 TYR 0.011 0.001 TYR B 135 ARG 0.004 0.000 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 259 time to evaluate : 1.619 Fit side-chains REVERT: A 30 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.6478 (p0) REVERT: A 112 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8378 (tm-30) REVERT: A 186 ASN cc_start: 0.8878 (m-40) cc_final: 0.8665 (m-40) REVERT: A 203 GLN cc_start: 0.8626 (tp40) cc_final: 0.8343 (tp40) REVERT: A 272 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8793 (mm-40) REVERT: A 273 MET cc_start: 0.8110 (ttm) cc_final: 0.7223 (ttm) REVERT: B 30 ASN cc_start: 0.7002 (OUTLIER) cc_final: 0.5806 (p0) REVERT: B 47 MET cc_start: 0.4203 (ttt) cc_final: 0.3782 (mtt) REVERT: B 273 MET cc_start: 0.8152 (ttm) cc_final: 0.7468 (ttm) REVERT: C 30 ASN cc_start: 0.6719 (OUTLIER) cc_final: 0.6093 (p0) REVERT: C 47 MET cc_start: 0.4581 (ttt) cc_final: 0.4312 (mtt) REVERT: C 115 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8916 (tp) REVERT: C 126 MET cc_start: 0.7862 (ttt) cc_final: 0.7562 (ttt) REVERT: C 127 PHE cc_start: 0.6819 (t80) cc_final: 0.6408 (t80) REVERT: C 272 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8755 (mm-40) REVERT: C 273 MET cc_start: 0.7994 (ttm) cc_final: 0.7787 (ttm) REVERT: D 30 ASN cc_start: 0.6665 (OUTLIER) cc_final: 0.5445 (p0) REVERT: D 47 MET cc_start: 0.3700 (ttt) cc_final: 0.3219 (mtt) REVERT: D 187 GLU cc_start: 0.7436 (tt0) cc_final: 0.7190 (tp30) REVERT: D 203 GLN cc_start: 0.8552 (tp40) cc_final: 0.8295 (tp40) REVERT: D 270 TYR cc_start: 0.9113 (m-80) cc_final: 0.8652 (m-80) REVERT: E 47 MET cc_start: 0.3439 (ttt) cc_final: 0.3232 (ttt) REVERT: E 146 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8612 (mm) REVERT: E 181 GLU cc_start: 0.8434 (tp30) cc_final: 0.8228 (tp30) REVERT: F 30 ASN cc_start: 0.7208 (OUTLIER) cc_final: 0.5992 (p0) REVERT: F 47 MET cc_start: 0.4543 (ttt) cc_final: 0.4162 (mtt) REVERT: F 112 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8141 (tm-30) REVERT: F 115 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8926 (tt) REVERT: G 30 ASN cc_start: 0.7064 (OUTLIER) cc_final: 0.6184 (p0) REVERT: G 274 ASP cc_start: 0.8009 (t0) cc_final: 0.7546 (t70) outliers start: 71 outliers final: 37 residues processed: 313 average time/residue: 0.2012 time to fit residues: 98.2088 Evaluate side-chains 284 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 238 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 116 optimal weight: 0.0870 chunk 0 optimal weight: 40.0000 chunk 86 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN E 149 GLN G 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 13748 Z= 0.222 Angle : 0.563 10.015 18641 Z= 0.290 Chirality : 0.044 0.370 2282 Planarity : 0.003 0.034 2366 Dihedral : 4.885 21.435 1939 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.30 % Allowed : 21.01 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.19), residues: 1764 helix: 1.00 (0.17), residues: 896 sheet: -1.51 (0.30), residues: 238 loop : -2.90 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 240 PHE 0.012 0.001 PHE E 178 TYR 0.007 0.001 TYR G 135 ARG 0.003 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 259 time to evaluate : 1.448 Fit side-chains REVERT: A 112 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8404 (tm-30) REVERT: A 157 THR cc_start: 0.9113 (t) cc_final: 0.8860 (m) REVERT: A 203 GLN cc_start: 0.8641 (tp40) cc_final: 0.8296 (tp40) REVERT: A 272 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8781 (mm-40) REVERT: A 273 MET cc_start: 0.8071 (ttm) cc_final: 0.7212 (ttm) REVERT: B 47 MET cc_start: 0.4226 (ttt) cc_final: 0.3789 (mtt) REVERT: B 273 MET cc_start: 0.8132 (ttm) cc_final: 0.7416 (ttm) REVERT: C 47 MET cc_start: 0.4573 (ttt) cc_final: 0.4289 (mtt) REVERT: C 115 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8884 (tp) REVERT: C 126 MET cc_start: 0.7849 (ttt) cc_final: 0.7554 (ttt) REVERT: C 127 PHE cc_start: 0.6820 (t80) cc_final: 0.6467 (t80) REVERT: C 138 LEU cc_start: 0.9025 (mp) cc_final: 0.8593 (mp) REVERT: C 273 MET cc_start: 0.8071 (ttm) cc_final: 0.7773 (ttm) REVERT: D 47 MET cc_start: 0.3704 (ttt) cc_final: 0.3224 (mtt) REVERT: D 115 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8743 (tp) REVERT: D 127 PHE cc_start: 0.7007 (t80) cc_final: 0.6642 (t80) REVERT: D 138 LEU cc_start: 0.8962 (mm) cc_final: 0.8729 (mt) REVERT: D 187 GLU cc_start: 0.7402 (tt0) cc_final: 0.7181 (tp30) REVERT: D 203 GLN cc_start: 0.8528 (tp40) cc_final: 0.8273 (tp40) REVERT: D 270 TYR cc_start: 0.9079 (m-80) cc_final: 0.8555 (m-80) REVERT: E 30 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.6428 (p0) REVERT: E 47 MET cc_start: 0.3663 (ttt) cc_final: 0.3425 (ttt) REVERT: E 69 LEU cc_start: 0.8814 (mm) cc_final: 0.8546 (tp) REVERT: E 181 GLU cc_start: 0.8365 (tp30) cc_final: 0.8148 (tp30) REVERT: E 267 SER cc_start: 0.8754 (t) cc_final: 0.8450 (p) REVERT: F 30 ASN cc_start: 0.7281 (OUTLIER) cc_final: 0.6067 (p0) REVERT: F 47 MET cc_start: 0.4145 (ttt) cc_final: 0.3735 (mtt) REVERT: F 112 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8302 (tm-30) REVERT: F 115 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8922 (tt) REVERT: F 272 GLN cc_start: 0.8962 (mm110) cc_final: 0.8678 (mm110) REVERT: G 30 ASN cc_start: 0.7051 (OUTLIER) cc_final: 0.6182 (p0) REVERT: G 134 GLU cc_start: 0.7812 (pm20) cc_final: 0.7514 (pm20) REVERT: G 274 ASP cc_start: 0.7996 (t0) cc_final: 0.7494 (t70) outliers start: 62 outliers final: 36 residues processed: 307 average time/residue: 0.1965 time to fit residues: 94.9465 Evaluate side-chains 285 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 243 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.1980 chunk 152 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN G 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 13748 Z= 0.188 Angle : 0.550 8.373 18641 Z= 0.282 Chirality : 0.043 0.378 2282 Planarity : 0.003 0.033 2366 Dihedral : 4.747 19.451 1939 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.74 % Allowed : 21.57 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.19), residues: 1764 helix: 1.20 (0.17), residues: 896 sheet: -1.30 (0.31), residues: 238 loop : -2.76 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 240 PHE 0.013 0.001 PHE D 277 TYR 0.008 0.001 TYR F 135 ARG 0.004 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 269 time to evaluate : 1.450 Fit side-chains REVERT: A 30 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6408 (p0) REVERT: A 112 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8432 (tm-30) REVERT: A 203 GLN cc_start: 0.8680 (tp40) cc_final: 0.8324 (tp40) REVERT: A 216 LEU cc_start: 0.9352 (mt) cc_final: 0.9087 (mt) REVERT: A 273 MET cc_start: 0.7944 (ttm) cc_final: 0.7071 (ttm) REVERT: B 30 ASN cc_start: 0.7030 (OUTLIER) cc_final: 0.5880 (p0) REVERT: B 47 MET cc_start: 0.4392 (ttt) cc_final: 0.3917 (mtt) REVERT: B 273 MET cc_start: 0.8134 (ttm) cc_final: 0.7400 (ttm) REVERT: C 30 ASN cc_start: 0.6594 (OUTLIER) cc_final: 0.6031 (p0) REVERT: C 47 MET cc_start: 0.4589 (ttt) cc_final: 0.4281 (mtt) REVERT: C 115 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8904 (tp) REVERT: C 126 MET cc_start: 0.7805 (ttt) cc_final: 0.7524 (ttt) REVERT: C 127 PHE cc_start: 0.6599 (t80) cc_final: 0.6326 (t80) REVERT: C 273 MET cc_start: 0.8072 (ttm) cc_final: 0.7767 (ttm) REVERT: D 30 ASN cc_start: 0.6602 (OUTLIER) cc_final: 0.5409 (p0) REVERT: D 47 MET cc_start: 0.3759 (ttt) cc_final: 0.3283 (mtt) REVERT: D 127 PHE cc_start: 0.6913 (t80) cc_final: 0.6549 (t80) REVERT: D 187 GLU cc_start: 0.7386 (tt0) cc_final: 0.7178 (tp30) REVERT: D 203 GLN cc_start: 0.8513 (tp40) cc_final: 0.8263 (tp40) REVERT: E 30 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.6428 (p0) REVERT: E 47 MET cc_start: 0.3720 (ttt) cc_final: 0.3464 (ttt) REVERT: E 157 THR cc_start: 0.8988 (t) cc_final: 0.8691 (m) REVERT: E 267 SER cc_start: 0.8607 (t) cc_final: 0.8329 (p) REVERT: F 47 MET cc_start: 0.4162 (ttt) cc_final: 0.3754 (mtt) REVERT: F 112 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8313 (tm-30) REVERT: F 115 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8898 (tt) REVERT: G 112 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8664 (tm-30) REVERT: G 134 GLU cc_start: 0.7710 (pm20) cc_final: 0.7400 (pm20) REVERT: G 274 ASP cc_start: 0.7956 (t0) cc_final: 0.7650 (t70) outliers start: 54 outliers final: 35 residues processed: 311 average time/residue: 0.1912 time to fit residues: 94.1061 Evaluate side-chains 288 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 246 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 GLN G 149 GLN G 200 GLN G 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13748 Z= 0.422 Angle : 0.651 7.761 18641 Z= 0.339 Chirality : 0.047 0.465 2282 Planarity : 0.003 0.033 2366 Dihedral : 5.023 23.737 1939 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.79 % Allowed : 21.91 % Favored : 73.30 % 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: -0.88 (0.19), residues: 1764 helix: 1.17 (0.16), residues: 896 sheet: -1.91 (0.28), residues: 224 loop : -2.69 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 240 PHE 0.018 0.002 PHE B 178 TYR 0.011 0.001 TYR D 135 ARG 0.006 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 238 time to evaluate : 1.484 Fit side-chains REVERT: A 30 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.6342 (p0) REVERT: A 112 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8463 (tm-30) REVERT: A 186 ASN cc_start: 0.8893 (m-40) cc_final: 0.8676 (m-40) REVERT: B 30 ASN cc_start: 0.6917 (OUTLIER) cc_final: 0.6050 (p0) REVERT: B 47 MET cc_start: 0.4275 (ttt) cc_final: 0.3846 (mtt) REVERT: B 112 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8429 (tm-30) REVERT: B 273 MET cc_start: 0.8184 (ttm) cc_final: 0.7489 (ttm) REVERT: C 30 ASN cc_start: 0.6888 (OUTLIER) cc_final: 0.6327 (p0) REVERT: C 47 MET cc_start: 0.4640 (ttt) cc_final: 0.4327 (mtt) REVERT: C 112 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8346 (tm-30) REVERT: C 115 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8992 (tp) REVERT: C 126 MET cc_start: 0.7839 (ttt) cc_final: 0.7575 (ttt) REVERT: C 273 MET cc_start: 0.8169 (ttm) cc_final: 0.7813 (ttm) REVERT: D 30 ASN cc_start: 0.6652 (OUTLIER) cc_final: 0.5424 (p0) REVERT: D 47 MET cc_start: 0.3739 (ttt) cc_final: 0.3291 (mtt) REVERT: D 115 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8859 (tp) REVERT: E 30 ASN cc_start: 0.7278 (OUTLIER) cc_final: 0.6743 (p0) REVERT: E 47 MET cc_start: 0.3727 (ttt) cc_final: 0.3505 (ttt) REVERT: E 69 LEU cc_start: 0.8774 (mm) cc_final: 0.8460 (tp) REVERT: E 157 THR cc_start: 0.9247 (t) cc_final: 0.8972 (m) REVERT: E 267 SER cc_start: 0.8872 (t) cc_final: 0.8565 (p) REVERT: F 30 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6379 (p0) REVERT: F 47 MET cc_start: 0.4483 (ttt) cc_final: 0.4084 (mtt) REVERT: F 112 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8414 (tm-30) REVERT: F 115 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8985 (tt) REVERT: G 30 ASN cc_start: 0.7077 (OUTLIER) cc_final: 0.6211 (p0) REVERT: G 112 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8702 (tm-30) outliers start: 69 outliers final: 46 residues processed: 298 average time/residue: 0.1881 time to fit residues: 88.9073 Evaluate side-chains 283 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 227 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 174 ASN Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 221 MET Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 50 optimal weight: 40.0000 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 0.0040 chunk 132 optimal weight: 5.9990 chunk 153 optimal weight: 30.0000 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13748 Z= 0.295 Angle : 0.624 9.712 18641 Z= 0.317 Chirality : 0.046 0.448 2282 Planarity : 0.003 0.032 2366 Dihedral : 4.923 21.703 1939 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.65 % Allowed : 22.61 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1764 helix: 1.27 (0.16), residues: 896 sheet: -1.90 (0.30), residues: 210 loop : -2.63 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 251 PHE 0.016 0.001 PHE B 178 TYR 0.012 0.001 TYR D 135 ARG 0.006 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 252 time to evaluate : 1.590 Fit side-chains REVERT: A 30 ASN cc_start: 0.7212 (OUTLIER) cc_final: 0.6279 (p0) REVERT: A 112 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 273 MET cc_start: 0.7571 (ttm) cc_final: 0.6994 (ttm) REVERT: B 30 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.6123 (p0) REVERT: B 47 MET cc_start: 0.4349 (ttt) cc_final: 0.3901 (mtt) REVERT: B 273 MET cc_start: 0.8146 (ttm) cc_final: 0.7355 (ttm) REVERT: C 30 ASN cc_start: 0.6812 (OUTLIER) cc_final: 0.6212 (p0) REVERT: C 47 MET cc_start: 0.4734 (ttt) cc_final: 0.4399 (mtt) REVERT: C 112 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 115 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8932 (tp) REVERT: C 126 MET cc_start: 0.7741 (ttt) cc_final: 0.7499 (ttt) REVERT: C 273 MET cc_start: 0.8137 (ttm) cc_final: 0.7774 (ttm) REVERT: D 30 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.5442 (p0) REVERT: D 47 MET cc_start: 0.3738 (ttt) cc_final: 0.3297 (mtt) REVERT: D 115 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8823 (tp) REVERT: D 278 LYS cc_start: 0.8314 (mmmm) cc_final: 0.8065 (mttp) REVERT: E 47 MET cc_start: 0.3763 (ttt) cc_final: 0.3512 (ttt) REVERT: E 69 LEU cc_start: 0.8803 (mm) cc_final: 0.8501 (tp) REVERT: E 157 THR cc_start: 0.9140 (t) cc_final: 0.8811 (m) REVERT: E 267 SER cc_start: 0.8868 (t) cc_final: 0.8530 (p) REVERT: F 30 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6033 (p0) REVERT: F 47 MET cc_start: 0.4409 (ttt) cc_final: 0.4023 (mtt) REVERT: F 112 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8471 (tm-30) REVERT: F 115 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8962 (tt) REVERT: G 30 ASN cc_start: 0.7039 (OUTLIER) cc_final: 0.6188 (p0) REVERT: G 134 GLU cc_start: 0.7824 (pm20) cc_final: 0.7485 (pm20) outliers start: 67 outliers final: 50 residues processed: 310 average time/residue: 0.1891 time to fit residues: 93.1551 Evaluate side-chains 301 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 242 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 221 MET Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13748 Z= 0.238 Angle : 0.630 10.466 18641 Z= 0.313 Chirality : 0.047 0.440 2282 Planarity : 0.003 0.031 2366 Dihedral : 4.826 20.382 1939 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.58 % Allowed : 23.30 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1764 helix: 1.36 (0.17), residues: 896 sheet: -1.80 (0.30), residues: 210 loop : -2.58 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 251 PHE 0.015 0.001 PHE B 178 TYR 0.012 0.001 TYR D 135 ARG 0.006 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 261 time to evaluate : 1.461 Fit side-chains REVERT: A 30 ASN cc_start: 0.7205 (OUTLIER) cc_final: 0.6299 (p0) REVERT: A 112 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 203 GLN cc_start: 0.8718 (tp40) cc_final: 0.8332 (tp40) REVERT: A 216 LEU cc_start: 0.9397 (mt) cc_final: 0.9143 (mt) REVERT: A 273 MET cc_start: 0.7539 (ttm) cc_final: 0.6970 (ttm) REVERT: B 30 ASN cc_start: 0.6974 (OUTLIER) cc_final: 0.6148 (p0) REVERT: B 47 MET cc_start: 0.4226 (ttt) cc_final: 0.3768 (mtt) REVERT: B 273 MET cc_start: 0.8117 (ttm) cc_final: 0.7335 (ttm) REVERT: C 30 ASN cc_start: 0.6824 (OUTLIER) cc_final: 0.6219 (p0) REVERT: C 47 MET cc_start: 0.4727 (ttt) cc_final: 0.4384 (mtt) REVERT: C 112 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8509 (tm-30) REVERT: C 115 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8997 (tt) REVERT: C 126 MET cc_start: 0.7724 (ttt) cc_final: 0.7501 (ttt) REVERT: C 273 MET cc_start: 0.8122 (ttm) cc_final: 0.7692 (ttm) REVERT: D 30 ASN cc_start: 0.6645 (OUTLIER) cc_final: 0.5406 (p0) REVERT: D 47 MET cc_start: 0.3712 (ttt) cc_final: 0.3288 (mtt) REVERT: D 115 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8786 (tp) REVERT: D 278 LYS cc_start: 0.8333 (mmmm) cc_final: 0.8087 (mttp) REVERT: E 30 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.6405 (p0) REVERT: E 47 MET cc_start: 0.3976 (ttt) cc_final: 0.3675 (ttt) REVERT: E 69 LEU cc_start: 0.8728 (mm) cc_final: 0.8365 (tp) REVERT: E 157 THR cc_start: 0.9025 (t) cc_final: 0.8662 (m) REVERT: E 267 SER cc_start: 0.8715 (t) cc_final: 0.8421 (p) REVERT: F 30 ASN cc_start: 0.7325 (OUTLIER) cc_final: 0.6142 (p0) REVERT: F 47 MET cc_start: 0.4425 (ttt) cc_final: 0.4034 (mtt) REVERT: F 112 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8503 (tm-30) REVERT: F 115 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8952 (tt) REVERT: G 30 ASN cc_start: 0.7059 (OUTLIER) cc_final: 0.6230 (p0) REVERT: G 134 GLU cc_start: 0.7781 (pm20) cc_final: 0.7470 (pm20) outliers start: 66 outliers final: 51 residues processed: 314 average time/residue: 0.1877 time to fit residues: 93.7276 Evaluate side-chains 311 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 250 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 221 MET Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13748 Z= 0.187 Angle : 0.625 11.632 18641 Z= 0.307 Chirality : 0.046 0.437 2282 Planarity : 0.003 0.031 2366 Dihedral : 4.685 18.286 1939 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.61 % Allowed : 24.55 % Favored : 71.84 % 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 (0.19), residues: 1764 helix: 1.54 (0.17), residues: 889 sheet: -1.34 (0.31), residues: 224 loop : -2.57 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 251 PHE 0.014 0.001 PHE B 178 TYR 0.012 0.001 TYR D 135 ARG 0.005 0.000 ARG A 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 276 time to evaluate : 1.574 Fit side-chains REVERT: A 30 ASN cc_start: 0.7224 (OUTLIER) cc_final: 0.6304 (p0) REVERT: A 112 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8498 (tm-30) REVERT: A 203 GLN cc_start: 0.8717 (tp40) cc_final: 0.8339 (tp40) REVERT: A 216 LEU cc_start: 0.9352 (mt) cc_final: 0.9103 (mt) REVERT: A 273 MET cc_start: 0.7486 (ttm) cc_final: 0.6898 (ttm) REVERT: B 30 ASN cc_start: 0.6976 (OUTLIER) cc_final: 0.6163 (p0) REVERT: B 47 MET cc_start: 0.4300 (ttt) cc_final: 0.3869 (mtt) REVERT: B 273 MET cc_start: 0.8046 (ttm) cc_final: 0.7598 (ttm) REVERT: B 274 ASP cc_start: 0.8082 (t70) cc_final: 0.7710 (t70) REVERT: C 30 ASN cc_start: 0.6849 (OUTLIER) cc_final: 0.6259 (p0) REVERT: C 47 MET cc_start: 0.4643 (ttt) cc_final: 0.4326 (mtt) REVERT: C 112 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8484 (tm-30) REVERT: C 126 MET cc_start: 0.7621 (ttt) cc_final: 0.7399 (ttt) REVERT: C 272 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8766 (mm110) REVERT: C 273 MET cc_start: 0.8116 (ttm) cc_final: 0.7865 (ttm) REVERT: D 30 ASN cc_start: 0.6573 (OUTLIER) cc_final: 0.5351 (p0) REVERT: D 47 MET cc_start: 0.3730 (ttt) cc_final: 0.3312 (mtt) REVERT: D 278 LYS cc_start: 0.8335 (mmmm) cc_final: 0.8089 (mttp) REVERT: E 30 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6399 (p0) REVERT: E 47 MET cc_start: 0.4058 (ttt) cc_final: 0.3824 (mtt) REVERT: E 65 VAL cc_start: 0.8531 (p) cc_final: 0.8309 (p) REVERT: E 69 LEU cc_start: 0.8699 (mm) cc_final: 0.8340 (tp) REVERT: E 157 THR cc_start: 0.9030 (t) cc_final: 0.8656 (m) REVERT: E 203 GLN cc_start: 0.8546 (tp40) cc_final: 0.8328 (tp40) REVERT: E 210 GLN cc_start: 0.8951 (tp40) cc_final: 0.8660 (mm-40) REVERT: E 267 SER cc_start: 0.8564 (t) cc_final: 0.8299 (p) REVERT: F 30 ASN cc_start: 0.7125 (OUTLIER) cc_final: 0.5999 (p0) REVERT: F 47 MET cc_start: 0.4327 (ttt) cc_final: 0.3931 (mtt) REVERT: F 112 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8509 (tm-30) REVERT: F 115 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8915 (tt) REVERT: G 30 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6268 (p0) REVERT: G 134 GLU cc_start: 0.7733 (pm20) cc_final: 0.7452 (pm20) outliers start: 52 outliers final: 34 residues processed: 322 average time/residue: 0.1890 time to fit residues: 95.6694 Evaluate side-chains 303 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 261 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 174 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 40.0000 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 30.0000 chunk 122 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108992 restraints weight = 19045.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112679 restraints weight = 10074.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115111 restraints weight = 6785.310| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13748 Z= 0.194 Angle : 0.633 11.713 18641 Z= 0.310 Chirality : 0.047 0.437 2282 Planarity : 0.003 0.032 2366 Dihedral : 4.644 17.958 1939 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.74 % Allowed : 25.10 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 1764 helix: 1.62 (0.16), residues: 889 sheet: -1.27 (0.31), residues: 224 loop : -2.54 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 240 PHE 0.014 0.001 PHE B 178 TYR 0.013 0.001 TYR D 135 ARG 0.006 0.000 ARG A 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2578.85 seconds wall clock time: 47 minutes 13.25 seconds (2833.25 seconds total)