Starting phenix.real_space_refine on Fri Mar 15 01:57:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/03_2024/8ew2_28640.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/03_2024/8ew2_28640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/03_2024/8ew2_28640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/03_2024/8ew2_28640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/03_2024/8ew2_28640.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew2_28640/03_2024/8ew2_28640.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.003 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 44 5.16 5 C 6516 2.51 5 N 1832 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "C ASP 17": "OD1" <-> "OD2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 218": "OD1" <-> "OD2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 10340 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "A" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "D" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Time building chain proxies: 5.83, per 1000 atoms: 0.56 Number of scatterers: 10340 At special positions: 0 Unit cell: (79.54, 97.58, 104.96, 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 44 16.00 O 1948 8.00 N 1832 7.00 C 6516 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: 4.18 Conformation dependent library (CDL) restraints added in 1.9 seconds 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2488 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 54.1% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 79 through 85 removed outlier: 3.968A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'B' and resid 244 through 260 removed outlier: 3.536A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 302 through 314 removed outlier: 6.790A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.585A pdb=" N ARG A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.984A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.540A pdb=" N THR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 312 removed outlier: 6.840A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 244 through 260 removed outlier: 3.552A pdb=" N THR C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 6.514A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.756A pdb=" N ILE D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 79 through 85 removed outlier: 3.968A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.525A pdb=" N THR D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 302 through 314 removed outlier: 6.314A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 340 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.586A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP B 143 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE B 185 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.805A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP A 143 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE A 185 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.959A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL C 267 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER C 300 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE C 269 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.310A pdb=" N GLY D 28 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE D 77 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 30 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL D 267 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER D 300 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N PHE D 269 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 571 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 4.51 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: 3441 1.34 - 1.46: 1498 1.46 - 1.57: 5536 1.57 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 10532 Sorted by residual: bond pdb=" CB PRO D 71 " pdb=" CG PRO D 71 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.67e+00 bond pdb=" C ASN C 70 " pdb=" N PRO C 71 " ideal model delta sigma weight residual 1.331 1.348 -0.017 7.90e-03 1.60e+04 4.55e+00 bond pdb=" C ASN A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.335 1.350 -0.015 9.40e-03 1.13e+04 2.40e+00 bond pdb=" CG1 ILE D 77 " pdb=" CD1 ILE D 77 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.00e+00 bond pdb=" CB GLN C 95 " pdb=" CG GLN C 95 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 ... (remaining 10527 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 340 107.07 - 113.80: 6037 113.80 - 120.52: 3955 120.52 - 127.25: 3822 127.25 - 133.98: 114 Bond angle restraints: 14268 Sorted by residual: angle pdb=" CA PRO D 71 " pdb=" N PRO D 71 " pdb=" CD PRO D 71 " ideal model delta sigma weight residual 112.00 105.58 6.42 1.40e+00 5.10e-01 2.10e+01 angle pdb=" N VAL B 23 " pdb=" CA VAL B 23 " pdb=" C VAL B 23 " ideal model delta sigma weight residual 106.21 110.54 -4.33 1.07e+00 8.73e-01 1.63e+01 angle pdb=" C THR A 51 " pdb=" N GLU A 52 " pdb=" CA GLU A 52 " ideal model delta sigma weight residual 120.82 125.63 -4.81 1.50e+00 4.44e-01 1.03e+01 angle pdb=" N GLU A 49 " pdb=" CA GLU A 49 " pdb=" C GLU A 49 " ideal model delta sigma weight residual 107.73 111.89 -4.16 1.34e+00 5.57e-01 9.63e+00 angle pdb=" N THR A 51 " pdb=" CA THR A 51 " pdb=" C THR A 51 " ideal model delta sigma weight residual 110.35 114.64 -4.29 1.40e+00 5.10e-01 9.39e+00 ... (remaining 14263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5508 17.98 - 35.97: 694 35.97 - 53.95: 167 53.95 - 71.94: 39 71.94 - 89.92: 12 Dihedral angle restraints: 6420 sinusoidal: 2540 harmonic: 3880 Sorted by residual: dihedral pdb=" CA ALA A 304 " pdb=" C ALA A 304 " pdb=" N LEU A 305 " pdb=" CA LEU A 305 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CB GLU B 132 " pdb=" CG GLU B 132 " pdb=" CD GLU B 132 " pdb=" OE1 GLU B 132 " ideal model delta sinusoidal sigma weight residual 0.00 -89.92 89.92 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CA ASP C 88 " pdb=" CB ASP C 88 " pdb=" CG ASP C 88 " pdb=" OD1 ASP C 88 " ideal model delta sinusoidal sigma weight residual -30.00 -86.17 56.17 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 6417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 936 0.026 - 0.051: 393 0.051 - 0.077: 158 0.077 - 0.102: 99 0.102 - 0.128: 42 Chirality restraints: 1628 Sorted by residual: chirality pdb=" CA ILE B 190 " pdb=" N ILE B 190 " pdb=" C ILE B 190 " pdb=" CB ILE B 190 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE D 182 " pdb=" N ILE D 182 " pdb=" C ILE D 182 " pdb=" CB ILE D 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA TYR C 84 " pdb=" N TYR C 84 " pdb=" C TYR C 84 " pdb=" CB TYR C 84 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1625 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 70 " 0.044 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO D 71 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 71 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 71 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 187 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A 188 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 8 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 9 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " -0.027 5.00e-02 4.00e+02 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 662 2.73 - 3.27: 10885 3.27 - 3.82: 19395 3.82 - 4.36: 23068 4.36 - 4.90: 38736 Nonbonded interactions: 92746 Sorted by model distance: nonbonded pdb=" OE1 GLU A 121 " pdb=" OG SER A 159 " model vdw 2.188 2.440 nonbonded pdb=" NZ LYS B 146 " pdb=" OE1 GLU B 187 " model vdw 2.216 2.520 nonbonded pdb=" OE1 GLU A 81 " pdb=" NE2 GLN A 85 " model vdw 2.220 2.520 nonbonded pdb=" NZ LYS C 207 " pdb=" O SER D 217 " model vdw 2.220 2.520 nonbonded pdb=" O GLN B 60 " pdb=" OG1 THR B 64 " model vdw 2.230 2.440 ... (remaining 92741 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 4.120 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 32.160 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 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: 0.020 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 10532 Z= 0.241 Angle : 0.626 10.619 14268 Z= 0.353 Chirality : 0.040 0.128 1628 Planarity : 0.005 0.064 1848 Dihedral : 17.049 89.921 3932 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.46 % Allowed : 21.72 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1340 helix: 1.69 (0.19), residues: 696 sheet: -1.46 (0.38), residues: 192 loop : -0.61 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 147 HIS 0.003 0.001 HIS B 80 PHE 0.010 0.001 PHE A 93 TYR 0.026 0.002 TYR B 58 ARG 0.006 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.054 Fit side-chains REVERT: C 84 TYR cc_start: 0.6279 (m-10) cc_final: 0.6030 (m-10) outliers start: 5 outliers final: 4 residues processed: 118 average time/residue: 0.2338 time to fit residues: 39.2154 Evaluate side-chains 109 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 77 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10532 Z= 0.214 Angle : 0.513 7.104 14268 Z= 0.263 Chirality : 0.039 0.127 1628 Planarity : 0.004 0.049 1848 Dihedral : 4.693 59.864 1460 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.55 % Allowed : 19.98 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.89 (0.24), residues: 1340 helix: 2.00 (0.19), residues: 692 sheet: -1.26 (0.35), residues: 216 loop : -0.66 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.004 0.001 HIS C 80 PHE 0.009 0.001 PHE A 93 TYR 0.016 0.002 TYR D 213 ARG 0.003 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.206 Fit side-chains REVERT: C 303 ARG cc_start: 0.7936 (ptt180) cc_final: 0.7229 (ttt180) REVERT: D 36 THR cc_start: 0.7189 (m) cc_final: 0.6963 (p) REVERT: D 173 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8942 (t80) outliers start: 28 outliers final: 16 residues processed: 140 average time/residue: 0.2621 time to fit residues: 50.0744 Evaluate side-chains 130 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.3980 chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10532 Z= 0.259 Angle : 0.514 6.046 14268 Z= 0.262 Chirality : 0.040 0.127 1628 Planarity : 0.004 0.052 1848 Dihedral : 4.154 20.050 1454 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.65 % Allowed : 18.43 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1340 helix: 2.02 (0.19), residues: 692 sheet: -1.32 (0.35), residues: 216 loop : -0.65 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 147 HIS 0.003 0.001 HIS C 80 PHE 0.010 0.002 PHE B 269 TYR 0.020 0.002 TYR D 213 ARG 0.003 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 123 time to evaluate : 1.189 Fit side-chains REVERT: A 57 PHE cc_start: 0.8103 (t80) cc_final: 0.7777 (t80) REVERT: A 106 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8779 (tt) REVERT: A 284 ASN cc_start: 0.9033 (t0) cc_final: 0.8773 (t0) REVERT: C 303 ARG cc_start: 0.7964 (ptt180) cc_final: 0.7317 (ttt180) REVERT: D 36 THR cc_start: 0.7231 (m) cc_final: 0.6995 (p) REVERT: D 173 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.9000 (t80) REVERT: D 295 TRP cc_start: 0.9039 (OUTLIER) cc_final: 0.7419 (m-90) outliers start: 51 outliers final: 33 residues processed: 154 average time/residue: 0.2508 time to fit residues: 52.5907 Evaluate side-chains 148 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 chunk 127 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10532 Z= 0.199 Angle : 0.485 6.457 14268 Z= 0.246 Chirality : 0.039 0.122 1628 Planarity : 0.004 0.046 1848 Dihedral : 3.988 19.600 1454 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.29 % Allowed : 19.25 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.24), residues: 1340 helix: 2.19 (0.19), residues: 692 sheet: -1.36 (0.34), residues: 216 loop : -0.64 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.003 0.000 HIS C 80 PHE 0.010 0.001 PHE C 144 TYR 0.016 0.001 TYR A 301 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 133 time to evaluate : 1.195 Fit side-chains REVERT: A 84 TYR cc_start: 0.7682 (m-80) cc_final: 0.7421 (m-10) REVERT: A 106 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8778 (tt) REVERT: A 284 ASN cc_start: 0.8988 (t0) cc_final: 0.8745 (t0) REVERT: C 303 ARG cc_start: 0.7964 (ptt180) cc_final: 0.7345 (ttt180) REVERT: D 173 TYR cc_start: 0.9137 (OUTLIER) cc_final: 0.8907 (t80) outliers start: 47 outliers final: 32 residues processed: 163 average time/residue: 0.2504 time to fit residues: 55.6375 Evaluate side-chains 150 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 116 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 88 optimal weight: 0.0270 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 10532 Z= 0.471 Angle : 0.635 5.736 14268 Z= 0.324 Chirality : 0.046 0.149 1628 Planarity : 0.005 0.049 1848 Dihedral : 4.548 28.732 1454 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.20 % Allowed : 18.43 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.23), residues: 1340 helix: 1.58 (0.19), residues: 692 sheet: -1.49 (0.40), residues: 164 loop : -0.93 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 147 HIS 0.004 0.001 HIS C 20 PHE 0.013 0.002 PHE B 144 TYR 0.032 0.002 TYR D 213 ARG 0.005 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 113 time to evaluate : 1.129 Fit side-chains REVERT: B 295 TRP cc_start: 0.9081 (OUTLIER) cc_final: 0.8695 (m-90) REVERT: A 106 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8749 (tt) REVERT: A 295 TRP cc_start: 0.9081 (OUTLIER) cc_final: 0.7460 (m-90) REVERT: C 34 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: C 295 TRP cc_start: 0.9118 (OUTLIER) cc_final: 0.7965 (m-90) REVERT: C 303 ARG cc_start: 0.8029 (ptt180) cc_final: 0.7449 (ttt180) REVERT: D 295 TRP cc_start: 0.9138 (OUTLIER) cc_final: 0.7538 (m-90) outliers start: 68 outliers final: 45 residues processed: 163 average time/residue: 0.2451 time to fit residues: 55.6829 Evaluate side-chains 152 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 101 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10532 Z= 0.226 Angle : 0.520 7.104 14268 Z= 0.263 Chirality : 0.040 0.127 1628 Planarity : 0.004 0.041 1848 Dihedral : 4.214 26.186 1454 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.29 % Allowed : 20.26 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.24), residues: 1340 helix: 1.93 (0.19), residues: 692 sheet: -1.29 (0.36), residues: 192 loop : -0.86 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.004 0.001 HIS C 80 PHE 0.010 0.001 PHE C 144 TYR 0.015 0.001 TYR A 213 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 123 time to evaluate : 1.255 Fit side-chains REVERT: B 295 TRP cc_start: 0.9057 (OUTLIER) cc_final: 0.8683 (m-90) REVERT: A 106 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8764 (tt) REVERT: A 332 LEU cc_start: 0.8569 (tt) cc_final: 0.8056 (mt) REVERT: C 34 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: C 303 ARG cc_start: 0.7975 (ptt180) cc_final: 0.7352 (ttt180) outliers start: 47 outliers final: 36 residues processed: 153 average time/residue: 0.2430 time to fit residues: 51.4346 Evaluate side-chains 152 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10532 Z= 0.230 Angle : 0.510 6.538 14268 Z= 0.260 Chirality : 0.040 0.127 1628 Planarity : 0.004 0.039 1848 Dihedral : 4.079 22.971 1454 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.20 % Allowed : 20.35 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.87 (0.24), residues: 1340 helix: 2.04 (0.19), residues: 692 sheet: -1.42 (0.34), residues: 216 loop : -0.70 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 147 HIS 0.006 0.001 HIS C 80 PHE 0.009 0.001 PHE C 144 TYR 0.022 0.001 TYR C 84 ARG 0.002 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 121 time to evaluate : 1.103 Fit side-chains REVERT: B 173 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.9102 (t80) REVERT: B 293 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8515 (mtmm) REVERT: B 295 TRP cc_start: 0.9070 (OUTLIER) cc_final: 0.8654 (m-90) REVERT: A 83 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8529 (tp) REVERT: A 106 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8787 (tt) REVERT: A 284 ASN cc_start: 0.9065 (t0) cc_final: 0.8795 (t0) REVERT: A 332 LEU cc_start: 0.8565 (tt) cc_final: 0.7946 (mt) REVERT: C 303 ARG cc_start: 0.7985 (ptt180) cc_final: 0.7376 (ttt180) REVERT: D 295 TRP cc_start: 0.9007 (OUTLIER) cc_final: 0.7340 (m-90) outliers start: 46 outliers final: 36 residues processed: 153 average time/residue: 0.2517 time to fit residues: 53.0955 Evaluate side-chains 155 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 113 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 0.0000 chunk 100 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10532 Z= 0.189 Angle : 0.495 6.035 14268 Z= 0.251 Chirality : 0.039 0.127 1628 Planarity : 0.004 0.038 1848 Dihedral : 3.917 21.010 1454 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.56 % Allowed : 21.26 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.04 (0.24), residues: 1340 helix: 2.22 (0.19), residues: 692 sheet: -1.41 (0.34), residues: 216 loop : -0.66 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 295 HIS 0.009 0.001 HIS C 80 PHE 0.009 0.001 PHE D 144 TYR 0.015 0.001 TYR D 213 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 123 time to evaluate : 1.252 Fit side-chains REVERT: B 57 PHE cc_start: 0.7781 (t80) cc_final: 0.7452 (t80) REVERT: B 173 TYR cc_start: 0.9283 (OUTLIER) cc_final: 0.9033 (t80) REVERT: B 293 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8457 (mtmm) REVERT: A 83 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8467 (tp) REVERT: A 106 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8765 (tt) REVERT: A 284 ASN cc_start: 0.9035 (t0) cc_final: 0.8780 (t0) REVERT: A 332 LEU cc_start: 0.8442 (tt) cc_final: 0.7949 (mt) REVERT: C 84 TYR cc_start: 0.6549 (m-10) cc_final: 0.6340 (m-10) REVERT: C 303 ARG cc_start: 0.7970 (ptt180) cc_final: 0.7393 (ttt180) outliers start: 39 outliers final: 33 residues processed: 149 average time/residue: 0.2482 time to fit residues: 51.1633 Evaluate side-chains 150 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 113 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 0.0670 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 125 optimal weight: 0.0870 chunk 76 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10532 Z= 0.176 Angle : 0.498 6.625 14268 Z= 0.252 Chirality : 0.038 0.122 1628 Planarity : 0.004 0.039 1848 Dihedral : 3.808 20.436 1454 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.56 % Allowed : 21.44 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.14 (0.24), residues: 1340 helix: 2.37 (0.19), residues: 692 sheet: -1.73 (0.37), residues: 176 loop : -0.65 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 295 HIS 0.008 0.001 HIS C 80 PHE 0.009 0.001 PHE D 144 TYR 0.015 0.001 TYR D 213 ARG 0.002 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 1.253 Fit side-chains REVERT: B 57 PHE cc_start: 0.7764 (t80) cc_final: 0.7438 (t80) REVERT: B 173 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.8982 (t80) REVERT: A 106 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8800 (tt) REVERT: A 284 ASN cc_start: 0.9013 (t0) cc_final: 0.8733 (t0) REVERT: A 332 LEU cc_start: 0.8420 (tt) cc_final: 0.7950 (mt) REVERT: C 84 TYR cc_start: 0.6231 (m-10) cc_final: 0.5981 (m-10) REVERT: C 303 ARG cc_start: 0.7962 (ptt180) cc_final: 0.7407 (ttt180) REVERT: C 317 LYS cc_start: 0.6762 (mptt) cc_final: 0.6331 (mttt) outliers start: 39 outliers final: 32 residues processed: 153 average time/residue: 0.2456 time to fit residues: 52.3625 Evaluate side-chains 154 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 ASN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10532 Z= 0.225 Angle : 0.518 6.474 14268 Z= 0.262 Chirality : 0.039 0.140 1628 Planarity : 0.004 0.038 1848 Dihedral : 3.845 21.874 1454 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.47 % Allowed : 22.17 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.16 (0.24), residues: 1340 helix: 2.34 (0.19), residues: 692 sheet: -1.37 (0.34), residues: 216 loop : -0.64 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 147 HIS 0.008 0.001 HIS C 80 PHE 0.010 0.001 PHE C 144 TYR 0.023 0.001 TYR D 213 ARG 0.002 0.000 ARG B 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 1.146 Fit side-chains REVERT: B 173 TYR cc_start: 0.9326 (OUTLIER) cc_final: 0.9064 (t80) REVERT: B 293 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8458 (mtmm) REVERT: B 295 TRP cc_start: 0.9091 (OUTLIER) cc_final: 0.8803 (m-90) REVERT: A 106 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8826 (tt) REVERT: A 284 ASN cc_start: 0.9049 (t0) cc_final: 0.8774 (t0) REVERT: A 332 LEU cc_start: 0.8455 (tt) cc_final: 0.7955 (mt) REVERT: C 84 TYR cc_start: 0.6349 (m-10) cc_final: 0.6049 (m-10) REVERT: C 173 TYR cc_start: 0.9266 (OUTLIER) cc_final: 0.9038 (t80) REVERT: C 303 ARG cc_start: 0.8022 (ptt180) cc_final: 0.7501 (ttt180) REVERT: C 317 LYS cc_start: 0.6957 (mptt) cc_final: 0.6346 (mttt) outliers start: 38 outliers final: 33 residues processed: 146 average time/residue: 0.2391 time to fit residues: 48.2790 Evaluate side-chains 154 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 338 CYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 CYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 13 optimal weight: 0.0470 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114472 restraints weight = 14024.023| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.88 r_work: 0.3239 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10532 Z= 0.229 Angle : 0.525 6.794 14268 Z= 0.265 Chirality : 0.039 0.147 1628 Planarity : 0.004 0.038 1848 Dihedral : 3.861 21.836 1454 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.74 % Allowed : 21.99 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.15 (0.24), residues: 1340 helix: 2.33 (0.19), residues: 692 sheet: -1.37 (0.34), residues: 216 loop : -0.64 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.007 0.001 HIS C 80 PHE 0.009 0.001 PHE A 144 TYR 0.021 0.001 TYR C 213 ARG 0.002 0.000 ARG B 258 =============================================================================== Job complete usr+sys time: 2228.32 seconds wall clock time: 41 minutes 17.51 seconds (2477.51 seconds total)