Starting phenix.real_space_refine on Wed Feb 14 21:33:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slq_10239/02_2024/6slq_10239.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slq_10239/02_2024/6slq_10239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slq_10239/02_2024/6slq_10239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slq_10239/02_2024/6slq_10239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slq_10239/02_2024/6slq_10239.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slq_10239/02_2024/6slq_10239.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 78 5.16 5 C 6508 2.51 5 N 1800 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 82": "NH1" <-> "NH2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "F ARG 18": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Time building chain proxies: 7.15, per 1000 atoms: 0.69 Number of scatterers: 10336 At special positions: 0 Unit cell: (115.9, 111.02, 84.18, 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 78 16.00 O 1950 8.00 N 1800 7.00 C 6508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=1.53 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 198 " - pdb=" SG CYS F 218 " distance=2.19 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 2.4 seconds 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 67.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.510A pdb=" N GLU A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.194A pdb=" N ASN A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.596A pdb=" N LYS B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.208A pdb=" N ALA B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.586A pdb=" N GLN B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.525A pdb=" N ILE B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.577A pdb=" N LYS B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN B 183 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.955A pdb=" N MET B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.605A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.616A pdb=" N MET C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 removed outlier: 3.627A pdb=" N MET C 66 " --> pdb=" O HIS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 160 through 174 removed outlier: 3.697A pdb=" N TYR C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.625A pdb=" N GLN C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.548A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 110 through 119 removed outlier: 3.720A pdb=" N GLN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 146 Processing helix chain 'D' and resid 160 through 173 Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.703A pdb=" N TRP D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 220 removed outlier: 3.533A pdb=" N GLY D 220 " --> pdb=" O THR D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 removed outlier: 3.634A pdb=" N MET E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 removed outlier: 4.008A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 removed outlier: 4.178A pdb=" N ALA E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.649A pdb=" N GLN E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 191 removed outlier: 4.188A pdb=" N TRP E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 210 through 218 removed outlier: 3.968A pdb=" N MET E 214 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS E 218 " --> pdb=" O MET E 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.730A pdb=" N LEU F 20 " --> pdb=" O SER F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 removed outlier: 3.546A pdb=" N MET F 66 " --> pdb=" O HIS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 119 removed outlier: 3.508A pdb=" N GLN F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 160 through 174 removed outlier: 3.554A pdb=" N TYR F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 186 Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.616A pdb=" N GLY F 206 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.716A pdb=" N GLN F 219 " --> pdb=" O MET F 215 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 3.570A pdb=" N VAL A 3 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 11 " --> pdb=" O VAL A 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 2 through 3 removed outlier: 4.465A pdb=" N VAL C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL C 11 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 2 through 4 removed outlier: 3.795A pdb=" N VAL D 3 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 11 " --> pdb=" O VAL D 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 2 through 3 removed outlier: 4.588A pdb=" N VAL F 3 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL F 11 " --> pdb=" O VAL F 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 577 hydrogen bonds defined for protein. 1731 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: 2.58 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.25: 1780 1.25 - 1.43: 2402 1.43 - 1.60: 6236 1.60 - 1.78: 0 1.78 - 1.95: 148 Bond restraints: 10566 Sorted by residual: bond pdb=" C SER F 146 " pdb=" N PRO F 147 " ideal model delta sigma weight residual 1.335 1.885 -0.550 1.36e-02 5.41e+03 1.63e+03 bond pdb=" C SER C 146 " pdb=" N PRO C 147 " ideal model delta sigma weight residual 1.335 1.849 -0.514 1.38e-02 5.25e+03 1.39e+03 bond pdb=" C SER E 146 " pdb=" N PRO E 147 " ideal model delta sigma weight residual 1.334 1.952 -0.618 2.34e-02 1.83e+03 6.97e+02 bond pdb=" C SER B 146 " pdb=" N PRO B 147 " ideal model delta sigma weight residual 1.334 1.842 -0.508 2.34e-02 1.83e+03 4.72e+02 bond pdb=" C PRO A 147 " pdb=" N THR A 148 " ideal model delta sigma weight residual 1.331 1.081 0.251 1.38e-02 5.25e+03 3.30e+02 ... (remaining 10561 not shown) Histogram of bond angle deviations from ideal: 100.54 - 109.10: 840 109.10 - 117.66: 7303 117.66 - 126.21: 5984 126.21 - 134.77: 229 134.77 - 143.32: 10 Bond angle restraints: 14366 Sorted by residual: angle pdb=" O SER C 146 " pdb=" C SER C 146 " pdb=" N PRO C 147 " ideal model delta sigma weight residual 121.31 136.36 -15.05 8.70e-01 1.32e+00 2.99e+02 angle pdb=" CA SER C 146 " pdb=" C SER C 146 " pdb=" N PRO C 147 " ideal model delta sigma weight residual 119.12 103.25 15.87 1.05e+00 9.07e-01 2.28e+02 angle pdb=" O SER F 146 " pdb=" C SER F 146 " pdb=" N PRO F 147 " ideal model delta sigma weight residual 121.31 133.91 -12.60 8.70e-01 1.32e+00 2.10e+02 angle pdb=" C SER C 146 " pdb=" N PRO C 147 " pdb=" CA PRO C 147 " ideal model delta sigma weight residual 119.24 104.23 15.01 1.04e+00 9.25e-01 2.08e+02 angle pdb=" O PRO C 147 " pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 122.18 136.81 -14.63 1.08e+00 8.57e-01 1.84e+02 ... (remaining 14361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6210 17.92 - 35.84: 275 35.84 - 53.76: 31 53.76 - 71.68: 2 71.68 - 89.60: 4 Dihedral angle restraints: 6522 sinusoidal: 2704 harmonic: 3818 Sorted by residual: dihedral pdb=" CB CYS C 198 " pdb=" SG CYS C 198 " pdb=" SG CYS C 218 " pdb=" CB CYS C 218 " ideal model delta sinusoidal sigma weight residual -86.00 -13.05 -72.95 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS F 198 " pdb=" SG CYS F 198 " pdb=" SG CYS F 218 " pdb=" CB CYS F 218 " ideal model delta sinusoidal sigma weight residual -86.00 -117.95 31.95 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" C PHE E 32 " pdb=" N PHE E 32 " pdb=" CA PHE E 32 " pdb=" CB PHE E 32 " ideal model delta harmonic sigma weight residual -122.60 -130.68 8.08 0 2.50e+00 1.60e-01 1.04e+01 ... (remaining 6519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1235 0.045 - 0.091: 273 0.091 - 0.136: 74 0.136 - 0.181: 16 0.181 - 0.226: 6 Chirality restraints: 1604 Sorted by residual: chirality pdb=" CA GLU B 29 " pdb=" N GLU B 29 " pdb=" C GLU B 29 " pdb=" CB GLU B 29 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA VAL F 27 " pdb=" N VAL F 27 " pdb=" C VAL F 27 " pdb=" CB VAL F 27 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA LYS C 30 " pdb=" N LYS C 30 " pdb=" C LYS C 30 " pdb=" CB LYS C 30 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1601 not shown) Planarity restraints: 1882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 147 " 0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C PRO E 147 " -0.085 2.00e-02 2.50e+03 pdb=" O PRO E 147 " 0.029 2.00e-02 2.50e+03 pdb=" N THR E 148 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 147 " 0.020 2.00e-02 2.50e+03 4.58e-02 2.09e+01 pdb=" C PRO A 147 " -0.079 2.00e-02 2.50e+03 pdb=" O PRO A 147 " 0.029 2.00e-02 2.50e+03 pdb=" N THR A 148 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 146 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C SER A 146 " 0.064 2.00e-02 2.50e+03 pdb=" O SER A 146 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO A 147 " -0.020 2.00e-02 2.50e+03 ... (remaining 1879 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 2 2.07 - 2.78: 2015 2.78 - 3.48: 14706 3.48 - 4.19: 22406 4.19 - 4.90: 39280 Nonbonded interactions: 78409 Sorted by model distance: nonbonded pdb=" O THR D 58 " pdb=" OE2 GLU E 35 " model vdw 1.359 3.040 nonbonded pdb=" O PRO F 17 " pdb=" OD1 ASN F 21 " model vdw 2.029 3.040 nonbonded pdb=" O PRO F 17 " pdb=" CG ASN F 21 " model vdw 2.202 3.270 nonbonded pdb=" NZ LYS C 30 " pdb=" OE2 GLU C 35 " model vdw 2.203 2.520 nonbonded pdb=" OE1 GLU C 71 " pdb=" OG1 THR D 210 " model vdw 2.211 2.440 ... (remaining 78404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'B' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'C' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'D' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'E' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'F' and (resid 1 through 17 or resid 19 through 220)) } 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=0.50 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.030 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.860 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.012 0.618 10566 Z= 0.815 Angle : 0.815 18.322 14366 Z= 0.578 Chirality : 0.045 0.226 1604 Planarity : 0.005 0.070 1882 Dihedral : 9.228 89.602 4028 Min Nonbonded Distance : 1.359 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.18 % Allowed : 5.04 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.02 (0.21), residues: 1310 helix: -0.14 (0.17), residues: 814 sheet: None (None), residues: 0 loop : -1.45 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 23 HIS 0.001 0.000 HIS E 62 PHE 0.012 0.001 PHE E 32 TYR 0.004 0.001 TYR B 130 ARG 0.002 0.000 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 604 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7711 (mtp) cc_final: 0.7431 (mtp) REVERT: A 100 ARG cc_start: 0.7453 (ttt180) cc_final: 0.7108 (ttp80) REVERT: A 109 SER cc_start: 0.8397 (m) cc_final: 0.8124 (p) REVERT: A 115 ILE cc_start: 0.8553 (mm) cc_final: 0.8338 (mm) REVERT: A 161 PHE cc_start: 0.8488 (t80) cc_final: 0.8099 (t80) REVERT: A 165 VAL cc_start: 0.9190 (p) cc_final: 0.8658 (p) REVERT: A 214 MET cc_start: 0.8981 (ptp) cc_final: 0.8585 (ppp) REVERT: A 215 MET cc_start: 0.8923 (mtm) cc_final: 0.7896 (mtp) REVERT: B 10 MET cc_start: 0.4214 (mmm) cc_final: 0.3837 (tmm) REVERT: B 30 LYS cc_start: 0.7477 (mttt) cc_final: 0.6371 (mttt) REVERT: B 50 GLN cc_start: 0.8163 (tt0) cc_final: 0.7652 (mt0) REVERT: B 96 MET cc_start: 0.5251 (mmt) cc_final: 0.4086 (mtt) REVERT: B 103 ASP cc_start: 0.8502 (m-30) cc_final: 0.8257 (m-30) REVERT: B 114 GLN cc_start: 0.8283 (pt0) cc_final: 0.7777 (pp30) REVERT: B 131 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7810 (mttt) REVERT: B 134 ILE cc_start: 0.9100 (mt) cc_final: 0.8881 (tp) REVERT: B 141 ILE cc_start: 0.8127 (mt) cc_final: 0.7527 (mt) REVERT: B 190 LEU cc_start: 0.9018 (mt) cc_final: 0.8747 (mt) REVERT: B 214 MET cc_start: 0.8598 (mtt) cc_final: 0.8234 (mmt) REVERT: C 24 VAL cc_start: 0.8228 (t) cc_final: 0.7139 (t) REVERT: C 25 LYS cc_start: 0.8264 (mttt) cc_final: 0.7648 (mtpt) REVERT: C 75 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8102 (tm-30) REVERT: C 98 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8481 (pp20) REVERT: C 100 ARG cc_start: 0.7433 (mmp-170) cc_final: 0.6802 (mtm110) REVERT: C 110 THR cc_start: 0.8097 (t) cc_final: 0.5248 (t) REVERT: C 113 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7033 (mp0) REVERT: C 115 ILE cc_start: 0.9639 (mt) cc_final: 0.9400 (tt) REVERT: C 211 LEU cc_start: 0.8283 (mm) cc_final: 0.7686 (mm) REVERT: D 63 GLN cc_start: 0.7804 (mp10) cc_final: 0.7447 (mp10) REVERT: D 213 GLU cc_start: 0.9185 (pt0) cc_final: 0.8942 (pm20) REVERT: D 215 MET cc_start: 0.8957 (mtm) cc_final: 0.8642 (mtm) REVERT: E 10 MET cc_start: 0.3988 (mmm) cc_final: 0.2448 (tmm) REVERT: E 96 MET cc_start: 0.3569 (mmp) cc_final: 0.2824 (mtt) REVERT: E 98 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6421 (mt-10) REVERT: E 124 ILE cc_start: 0.7377 (mm) cc_final: 0.6823 (mt) REVERT: E 134 ILE cc_start: 0.9165 (mt) cc_final: 0.8826 (tp) REVERT: F 25 LYS cc_start: 0.8750 (mttt) cc_final: 0.8174 (mtpt) REVERT: F 68 MET cc_start: 0.7554 (mtp) cc_final: 0.7181 (mtm) REVERT: F 75 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8299 (tm-30) REVERT: F 100 ARG cc_start: 0.7685 (mmp-170) cc_final: 0.6996 (mtm110) REVERT: F 110 THR cc_start: 0.7649 (t) cc_final: 0.7441 (t) REVERT: F 117 TRP cc_start: 0.8519 (m-10) cc_final: 0.7511 (m-10) REVERT: F 133 TRP cc_start: 0.8221 (m-10) cc_final: 0.7316 (m-10) outliers start: 2 outliers final: 0 residues processed: 604 average time/residue: 0.2905 time to fit residues: 231.4843 Evaluate side-chains 363 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 30.0000 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS B 9 GLN B 95 GLN B 114 GLN B 179 GLN C 4 GLN C 53 ASN C 84 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 9 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN F 4 GLN F 53 ASN F 84 HIS ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 10566 Z= 0.307 Angle : 0.696 6.757 14366 Z= 0.364 Chirality : 0.045 0.211 1604 Planarity : 0.006 0.049 1882 Dihedral : 3.619 17.977 1404 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.27 % Allowed : 3.36 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.27 (0.22), residues: 1310 helix: 0.34 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -1.05 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 133 HIS 0.006 0.001 HIS B 62 PHE 0.024 0.002 PHE F 168 TYR 0.016 0.002 TYR D 130 ARG 0.007 0.001 ARG E 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 428 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7422 (ttt180) cc_final: 0.7115 (ttp80) REVERT: A 133 TRP cc_start: 0.8610 (m-10) cc_final: 0.8195 (m-10) REVERT: A 161 PHE cc_start: 0.8677 (t80) cc_final: 0.8258 (t80) REVERT: A 179 GLN cc_start: 0.8571 (tp-100) cc_final: 0.8092 (tp-100) REVERT: A 214 MET cc_start: 0.9190 (ptp) cc_final: 0.8740 (ppp) REVERT: A 215 MET cc_start: 0.8961 (mtm) cc_final: 0.8441 (ptm) REVERT: B 50 GLN cc_start: 0.8374 (tt0) cc_final: 0.7356 (mt0) REVERT: B 96 MET cc_start: 0.5240 (mmt) cc_final: 0.3932 (mtt) REVERT: B 141 ILE cc_start: 0.8343 (mt) cc_final: 0.7998 (mt) REVERT: B 164 TYR cc_start: 0.8588 (t80) cc_final: 0.8099 (t80) REVERT: B 176 GLN cc_start: 0.8480 (mp10) cc_final: 0.8079 (mp10) REVERT: B 180 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8571 (pm20) REVERT: B 190 LEU cc_start: 0.9195 (mt) cc_final: 0.8811 (mt) REVERT: B 214 MET cc_start: 0.8564 (mtt) cc_final: 0.8158 (mmt) REVERT: C 28 GLU cc_start: 0.7760 (mp0) cc_final: 0.7421 (mt-10) REVERT: C 100 ARG cc_start: 0.7866 (mmp-170) cc_final: 0.7144 (mtm110) REVERT: C 104 ILE cc_start: 0.8525 (tt) cc_final: 0.7946 (tp) REVERT: C 113 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7201 (mt-10) REVERT: C 131 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8309 (tttt) REVERT: C 132 ARG cc_start: 0.8435 (ptp-170) cc_final: 0.8178 (ptp-170) REVERT: C 133 TRP cc_start: 0.8275 (m-10) cc_final: 0.7325 (m-10) REVERT: D 10 MET cc_start: 0.6769 (mmm) cc_final: 0.4618 (ttt) REVERT: D 96 MET cc_start: 0.3097 (mmp) cc_final: 0.2327 (mmt) REVERT: D 213 GLU cc_start: 0.9160 (pt0) cc_final: 0.8808 (pm20) REVERT: E 10 MET cc_start: 0.4020 (mmm) cc_final: 0.3361 (tmm) REVERT: E 50 GLN cc_start: 0.8622 (mt0) cc_final: 0.8373 (mt0) REVERT: E 84 HIS cc_start: 0.7474 (t-170) cc_final: 0.6988 (t-170) REVERT: E 96 MET cc_start: 0.4011 (mmp) cc_final: 0.2837 (mtt) REVERT: E 112 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8320 (tp40) REVERT: E 141 ILE cc_start: 0.8418 (mt) cc_final: 0.8128 (mt) REVERT: E 144 MET cc_start: 0.8155 (ppp) cc_final: 0.7734 (ppp) REVERT: F 18 ARG cc_start: 0.8680 (ttm-80) cc_final: 0.8342 (ttm-80) REVERT: F 25 LYS cc_start: 0.8878 (mttt) cc_final: 0.8547 (tttm) REVERT: F 39 MET cc_start: 0.7770 (tpp) cc_final: 0.7566 (ttm) REVERT: F 104 ILE cc_start: 0.8491 (tt) cc_final: 0.8275 (tp) REVERT: F 131 LYS cc_start: 0.8871 (ttmm) cc_final: 0.8509 (tttp) REVERT: F 211 LEU cc_start: 0.9239 (mm) cc_final: 0.9027 (mm) outliers start: 3 outliers final: 0 residues processed: 428 average time/residue: 0.2674 time to fit residues: 150.7918 Evaluate side-chains 328 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 0.4980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN B 179 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 67 GLN E 74 ASN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10566 Z= 0.248 Angle : 0.634 6.415 14366 Z= 0.328 Chirality : 0.045 0.186 1604 Planarity : 0.005 0.056 1882 Dihedral : 3.734 16.703 1404 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.15 (0.22), residues: 1310 helix: 0.39 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -0.92 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 133 HIS 0.005 0.001 HIS A 12 PHE 0.022 0.002 PHE C 168 TYR 0.017 0.002 TYR F 169 ARG 0.008 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 422 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7364 (pm20) cc_final: 0.7150 (tm-30) REVERT: A 133 TRP cc_start: 0.8542 (m-10) cc_final: 0.7986 (m-10) REVERT: A 161 PHE cc_start: 0.8693 (t80) cc_final: 0.8291 (t80) REVERT: A 212 GLU cc_start: 0.9219 (pt0) cc_final: 0.8696 (pm20) REVERT: A 214 MET cc_start: 0.9162 (ptp) cc_final: 0.8781 (ppp) REVERT: A 215 MET cc_start: 0.8540 (mtm) cc_final: 0.8218 (ptp) REVERT: B 10 MET cc_start: 0.4827 (tmm) cc_final: 0.4251 (tmm) REVERT: B 50 GLN cc_start: 0.8390 (tt0) cc_final: 0.7338 (mt0) REVERT: B 211 LEU cc_start: 0.8927 (tp) cc_final: 0.8213 (tp) REVERT: B 214 MET cc_start: 0.8544 (mtt) cc_final: 0.8059 (mmp) REVERT: C 21 ASN cc_start: 0.8236 (m110) cc_final: 0.7822 (m110) REVERT: C 100 ARG cc_start: 0.8050 (mmp-170) cc_final: 0.7376 (mtm110) REVERT: C 104 ILE cc_start: 0.8577 (tt) cc_final: 0.8256 (tp) REVERT: C 131 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8352 (tttp) REVERT: C 173 ARG cc_start: 0.8515 (ttp-170) cc_final: 0.8280 (ttp-170) REVERT: D 40 PHE cc_start: 0.8768 (t80) cc_final: 0.8491 (t80) REVERT: D 68 MET cc_start: 0.8208 (mtp) cc_final: 0.7596 (mtt) REVERT: D 96 MET cc_start: 0.3401 (mmp) cc_final: 0.2990 (mmt) REVERT: D 131 LYS cc_start: 0.8582 (tttt) cc_final: 0.8345 (tttt) REVERT: D 212 GLU cc_start: 0.9063 (pt0) cc_final: 0.8134 (pm20) REVERT: D 213 GLU cc_start: 0.9108 (pt0) cc_final: 0.8765 (pm20) REVERT: D 215 MET cc_start: 0.8367 (mtm) cc_final: 0.7220 (mmt) REVERT: E 10 MET cc_start: 0.4211 (mmm) cc_final: 0.3437 (tmm) REVERT: E 50 GLN cc_start: 0.8498 (mt0) cc_final: 0.8183 (mt0) REVERT: E 96 MET cc_start: 0.4340 (mmp) cc_final: 0.2892 (mtt) REVERT: E 112 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8499 (tp40) REVERT: E 202 LEU cc_start: 0.8718 (mm) cc_final: 0.8333 (pp) REVERT: E 214 MET cc_start: 0.8928 (mtp) cc_final: 0.8279 (tpt) REVERT: E 215 MET cc_start: 0.8261 (mtt) cc_final: 0.7988 (mtt) REVERT: F 18 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8336 (ttm-80) REVERT: F 21 ASN cc_start: 0.8385 (m110) cc_final: 0.8151 (m110) REVERT: F 25 LYS cc_start: 0.8826 (mttt) cc_final: 0.8569 (tttm) REVERT: F 55 MET cc_start: 0.8250 (ptp) cc_final: 0.8032 (ptm) REVERT: F 110 THR cc_start: 0.8268 (t) cc_final: 0.7640 (t) REVERT: F 115 ILE cc_start: 0.9635 (mt) cc_final: 0.9308 (tt) REVERT: F 131 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8611 (tttt) REVERT: F 140 LYS cc_start: 0.8089 (tppt) cc_final: 0.7797 (tttt) REVERT: F 144 MET cc_start: 0.6368 (tmm) cc_final: 0.5592 (ttt) outliers start: 1 outliers final: 0 residues processed: 422 average time/residue: 0.2619 time to fit residues: 148.3835 Evaluate side-chains 332 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN C 139 ASN D 87 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN F 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10566 Z= 0.188 Angle : 0.615 8.823 14366 Z= 0.310 Chirality : 0.044 0.201 1604 Planarity : 0.005 0.053 1882 Dihedral : 3.787 23.602 1404 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.35 % Allowed : 2.83 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.14 (0.22), residues: 1310 helix: 0.63 (0.17), residues: 854 sheet: None (None), residues: 0 loop : -0.81 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 117 HIS 0.006 0.001 HIS A 12 PHE 0.024 0.002 PHE F 161 TYR 0.010 0.001 TYR B 145 ARG 0.007 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 426 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6214 (mmm) cc_final: 0.4877 (ttt) REVERT: A 118 MET cc_start: 0.8107 (mtt) cc_final: 0.7891 (mmm) REVERT: A 128 GLU cc_start: 0.7536 (pm20) cc_final: 0.7120 (tm-30) REVERT: A 161 PHE cc_start: 0.8655 (t80) cc_final: 0.8316 (t80) REVERT: A 167 ARG cc_start: 0.8822 (ptm160) cc_final: 0.8518 (ptm160) REVERT: A 212 GLU cc_start: 0.9097 (pt0) cc_final: 0.8888 (pm20) REVERT: A 214 MET cc_start: 0.9110 (ptp) cc_final: 0.8760 (ppp) REVERT: A 215 MET cc_start: 0.8441 (mtm) cc_final: 0.8140 (ptp) REVERT: B 10 MET cc_start: 0.4940 (tmm) cc_final: 0.4486 (tmm) REVERT: B 50 GLN cc_start: 0.8407 (tt0) cc_final: 0.7598 (mt0) REVERT: B 81 ASP cc_start: 0.7328 (m-30) cc_final: 0.7086 (m-30) REVERT: B 115 ILE cc_start: 0.8765 (mt) cc_final: 0.8203 (mt) REVERT: B 118 MET cc_start: 0.8427 (ptt) cc_final: 0.7790 (tpp) REVERT: B 141 ILE cc_start: 0.8642 (mt) cc_final: 0.8412 (mt) REVERT: B 164 TYR cc_start: 0.8295 (t80) cc_final: 0.8016 (t80) REVERT: B 193 ASN cc_start: 0.6185 (m110) cc_final: 0.5063 (m110) REVERT: B 211 LEU cc_start: 0.8964 (tp) cc_final: 0.8192 (tp) REVERT: B 214 MET cc_start: 0.8536 (mtt) cc_final: 0.8044 (mmp) REVERT: C 21 ASN cc_start: 0.8076 (m110) cc_final: 0.7655 (m-40) REVERT: C 100 ARG cc_start: 0.7972 (mmp-170) cc_final: 0.7376 (mtm110) REVERT: C 104 ILE cc_start: 0.8504 (tt) cc_final: 0.7977 (tp) REVERT: C 131 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8449 (tttp) REVERT: C 133 TRP cc_start: 0.8029 (m-10) cc_final: 0.7056 (m-10) REVERT: C 173 ARG cc_start: 0.8375 (ttp-170) cc_final: 0.8056 (ttp-170) REVERT: C 176 GLN cc_start: 0.8046 (pm20) cc_final: 0.7837 (pm20) REVERT: D 10 MET cc_start: 0.6493 (mmm) cc_final: 0.4824 (ttt) REVERT: D 40 PHE cc_start: 0.8638 (t80) cc_final: 0.8289 (t80) REVERT: D 57 ASN cc_start: 0.8999 (m-40) cc_final: 0.8703 (m-40) REVERT: D 66 MET cc_start: 0.8905 (mmm) cc_final: 0.8568 (mmm) REVERT: D 96 MET cc_start: 0.3254 (mmp) cc_final: 0.3020 (mmt) REVERT: D 131 LYS cc_start: 0.8616 (tttt) cc_final: 0.8355 (tttt) REVERT: D 212 GLU cc_start: 0.9019 (pt0) cc_final: 0.7837 (pm20) REVERT: E 10 MET cc_start: 0.4269 (mmm) cc_final: 0.3508 (tmm) REVERT: E 50 GLN cc_start: 0.8506 (mt0) cc_final: 0.8221 (mt0) REVERT: E 96 MET cc_start: 0.4506 (mmp) cc_final: 0.2976 (mtt) REVERT: E 98 GLU cc_start: 0.8324 (tp30) cc_final: 0.8090 (tp30) REVERT: E 112 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8479 (tp40) REVERT: E 202 LEU cc_start: 0.8722 (mm) cc_final: 0.8331 (pp) REVERT: E 212 GLU cc_start: 0.8435 (pm20) cc_final: 0.8179 (pm20) REVERT: E 214 MET cc_start: 0.9001 (mtp) cc_final: 0.8557 (tpt) REVERT: F 18 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8150 (ttm-80) REVERT: F 25 LYS cc_start: 0.8889 (mttt) cc_final: 0.8594 (tttm) REVERT: F 110 THR cc_start: 0.8340 (t) cc_final: 0.7897 (t) REVERT: F 117 TRP cc_start: 0.8213 (m-10) cc_final: 0.7558 (m-10) REVERT: F 131 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8403 (tttp) REVERT: F 140 LYS cc_start: 0.8061 (tppt) cc_final: 0.7685 (tttt) REVERT: F 144 MET cc_start: 0.6466 (tmm) cc_final: 0.5700 (ttt) outliers start: 4 outliers final: 0 residues processed: 426 average time/residue: 0.2646 time to fit residues: 154.2280 Evaluate side-chains 329 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 88 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.0670 chunk 114 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 195 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10566 Z= 0.188 Angle : 0.607 7.269 14366 Z= 0.306 Chirality : 0.044 0.151 1604 Planarity : 0.005 0.052 1882 Dihedral : 3.823 19.150 1404 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.09 % Allowed : 1.50 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1310 helix: 0.68 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -0.47 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 117 HIS 0.005 0.001 HIS A 12 PHE 0.016 0.002 PHE D 161 TYR 0.013 0.001 TYR E 164 ARG 0.005 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 421 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6318 (mmm) cc_final: 0.4926 (ttt) REVERT: A 23 TRP cc_start: 0.8464 (t-100) cc_final: 0.7882 (t-100) REVERT: A 55 MET cc_start: 0.8979 (ttm) cc_final: 0.8776 (ttp) REVERT: A 128 GLU cc_start: 0.7682 (pm20) cc_final: 0.7477 (tm-30) REVERT: A 131 LYS cc_start: 0.8535 (tttt) cc_final: 0.8216 (tptm) REVERT: A 154 ARG cc_start: 0.7138 (mtm-85) cc_final: 0.5869 (mtm-85) REVERT: A 161 PHE cc_start: 0.8690 (t80) cc_final: 0.8339 (t80) REVERT: A 212 GLU cc_start: 0.9093 (pt0) cc_final: 0.8797 (pm20) REVERT: A 214 MET cc_start: 0.9183 (ptp) cc_final: 0.8742 (ppp) REVERT: A 215 MET cc_start: 0.8566 (mtm) cc_final: 0.8129 (ptp) REVERT: B 9 GLN cc_start: 0.5073 (tp40) cc_final: 0.4818 (tp-100) REVERT: B 10 MET cc_start: 0.5005 (tmm) cc_final: 0.4545 (tmm) REVERT: B 50 GLN cc_start: 0.8361 (tt0) cc_final: 0.7784 (mt0) REVERT: B 63 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8141 (mm-40) REVERT: B 68 MET cc_start: 0.7976 (tpp) cc_final: 0.7757 (tpp) REVERT: B 70 LYS cc_start: 0.8852 (ptmt) cc_final: 0.8636 (pttt) REVERT: B 141 ILE cc_start: 0.8666 (mt) cc_final: 0.8396 (mt) REVERT: B 214 MET cc_start: 0.8490 (mtt) cc_final: 0.7988 (mmp) REVERT: C 28 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7083 (mp0) REVERT: C 100 ARG cc_start: 0.8010 (mmp-170) cc_final: 0.7471 (mtm110) REVERT: C 104 ILE cc_start: 0.8528 (tt) cc_final: 0.7970 (tp) REVERT: C 115 ILE cc_start: 0.9556 (mt) cc_final: 0.9331 (tt) REVERT: C 131 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8252 (tttp) REVERT: C 133 TRP cc_start: 0.7958 (m-10) cc_final: 0.7010 (m-10) REVERT: C 173 ARG cc_start: 0.8436 (ttp-170) cc_final: 0.7888 (ttp-170) REVERT: D 10 MET cc_start: 0.6352 (mmm) cc_final: 0.4888 (ttt) REVERT: D 40 PHE cc_start: 0.8638 (t80) cc_final: 0.8324 (t80) REVERT: D 96 MET cc_start: 0.3087 (mmp) cc_final: 0.2842 (mmt) REVERT: D 114 GLN cc_start: 0.9252 (pt0) cc_final: 0.8879 (pt0) REVERT: D 118 MET cc_start: 0.8298 (mtt) cc_final: 0.8066 (mmm) REVERT: D 131 LYS cc_start: 0.8492 (tttt) cc_final: 0.8052 (tptm) REVERT: E 10 MET cc_start: 0.4271 (mmm) cc_final: 0.3545 (tmm) REVERT: E 16 SER cc_start: 0.8701 (m) cc_final: 0.8475 (p) REVERT: E 50 GLN cc_start: 0.8477 (mt0) cc_final: 0.8137 (mt0) REVERT: E 98 GLU cc_start: 0.8292 (tp30) cc_final: 0.7701 (tp30) REVERT: E 112 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8534 (tp40) REVERT: E 115 ILE cc_start: 0.8789 (mt) cc_final: 0.8285 (mt) REVERT: E 118 MET cc_start: 0.8420 (ptt) cc_final: 0.7583 (tpp) REVERT: E 202 LEU cc_start: 0.8727 (mm) cc_final: 0.8296 (pp) REVERT: E 214 MET cc_start: 0.8928 (mtp) cc_final: 0.8538 (tpt) REVERT: F 25 LYS cc_start: 0.8902 (mttt) cc_final: 0.8574 (tttm) REVERT: F 131 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8619 (tttp) REVERT: F 140 LYS cc_start: 0.8035 (tppt) cc_final: 0.7579 (tttt) REVERT: F 144 MET cc_start: 0.6484 (tmm) cc_final: 0.5766 (ttt) outliers start: 1 outliers final: 0 residues processed: 421 average time/residue: 0.2611 time to fit residues: 148.2254 Evaluate side-chains 322 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10566 Z= 0.257 Angle : 0.655 11.152 14366 Z= 0.339 Chirality : 0.045 0.136 1604 Planarity : 0.005 0.055 1882 Dihedral : 4.012 17.675 1404 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.27 % Allowed : 2.04 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.20 (0.22), residues: 1310 helix: 0.55 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -0.53 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 117 HIS 0.009 0.001 HIS E 62 PHE 0.018 0.002 PHE D 161 TYR 0.014 0.002 TYR B 164 ARG 0.005 0.001 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 398 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6627 (mmm) cc_final: 0.5260 (ttt) REVERT: A 128 GLU cc_start: 0.7668 (pm20) cc_final: 0.7307 (tm-30) REVERT: A 161 PHE cc_start: 0.8740 (t80) cc_final: 0.8361 (t80) REVERT: A 212 GLU cc_start: 0.9131 (pt0) cc_final: 0.8822 (pm20) REVERT: A 214 MET cc_start: 0.9198 (ptp) cc_final: 0.8783 (ppp) REVERT: A 215 MET cc_start: 0.8547 (mtm) cc_final: 0.8055 (mtm) REVERT: B 10 MET cc_start: 0.5328 (tmm) cc_final: 0.4514 (tmm) REVERT: B 50 GLN cc_start: 0.8422 (tt0) cc_final: 0.7652 (mt0) REVERT: B 63 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8140 (mm-40) REVERT: B 67 GLN cc_start: 0.8446 (tp-100) cc_final: 0.8065 (mm-40) REVERT: B 115 ILE cc_start: 0.8866 (mt) cc_final: 0.8661 (mt) REVERT: B 118 MET cc_start: 0.8533 (ptt) cc_final: 0.7644 (tpp) REVERT: B 141 ILE cc_start: 0.8779 (mt) cc_final: 0.8440 (mt) REVERT: B 144 MET cc_start: 0.8475 (ppp) cc_final: 0.8154 (ppp) REVERT: B 214 MET cc_start: 0.8541 (mtt) cc_final: 0.8138 (mmp) REVERT: B 215 MET cc_start: 0.8098 (mtm) cc_final: 0.7007 (mtm) REVERT: C 100 ARG cc_start: 0.8060 (mmp-170) cc_final: 0.7696 (mtm110) REVERT: C 104 ILE cc_start: 0.8458 (tt) cc_final: 0.7940 (tp) REVERT: C 132 ARG cc_start: 0.8393 (ptp-170) cc_final: 0.7840 (ttp-110) REVERT: C 133 TRP cc_start: 0.7999 (m-10) cc_final: 0.6996 (m-10) REVERT: C 143 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7923 (ttm170) REVERT: D 68 MET cc_start: 0.8288 (mtt) cc_final: 0.7949 (mtt) REVERT: D 96 MET cc_start: 0.2960 (mmp) cc_final: 0.2551 (mmt) REVERT: D 114 GLN cc_start: 0.9285 (pt0) cc_final: 0.8910 (pt0) REVERT: D 118 MET cc_start: 0.8349 (mtt) cc_final: 0.7919 (mmm) REVERT: D 199 LYS cc_start: 0.8970 (ptpt) cc_final: 0.8656 (pttt) REVERT: E 10 MET cc_start: 0.4375 (mmm) cc_final: 0.3668 (tmm) REVERT: E 50 GLN cc_start: 0.8572 (mt0) cc_final: 0.8348 (mt0) REVERT: E 112 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8448 (tp40) REVERT: E 202 LEU cc_start: 0.8705 (mm) cc_final: 0.8410 (pp) REVERT: E 214 MET cc_start: 0.9001 (mtp) cc_final: 0.8386 (tpt) REVERT: F 25 LYS cc_start: 0.8782 (mttt) cc_final: 0.8400 (tttm) REVERT: F 69 LEU cc_start: 0.8581 (pp) cc_final: 0.8280 (pp) REVERT: F 100 ARG cc_start: 0.8994 (mtp180) cc_final: 0.8574 (mtm110) REVERT: F 140 LYS cc_start: 0.8013 (tppt) cc_final: 0.7691 (tttt) outliers start: 3 outliers final: 0 residues processed: 398 average time/residue: 0.2572 time to fit residues: 137.8487 Evaluate side-chains 317 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.0010 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN F 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10566 Z= 0.175 Angle : 0.624 9.252 14366 Z= 0.314 Chirality : 0.044 0.153 1604 Planarity : 0.005 0.051 1882 Dihedral : 3.895 15.670 1404 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1310 helix: 0.76 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.40 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 117 HIS 0.006 0.001 HIS A 12 PHE 0.014 0.002 PHE E 161 TYR 0.017 0.001 TYR F 164 ARG 0.014 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6513 (mmm) cc_final: 0.5120 (ttt) REVERT: A 40 PHE cc_start: 0.8586 (t80) cc_final: 0.8364 (t80) REVERT: A 68 MET cc_start: 0.8634 (mmt) cc_final: 0.7233 (mmt) REVERT: A 128 GLU cc_start: 0.7614 (pm20) cc_final: 0.7259 (tm-30) REVERT: A 131 LYS cc_start: 0.8473 (tttt) cc_final: 0.8255 (tptm) REVERT: A 144 MET cc_start: 0.7997 (ppp) cc_final: 0.7723 (ptt) REVERT: A 161 PHE cc_start: 0.8679 (t80) cc_final: 0.8317 (t80) REVERT: A 214 MET cc_start: 0.9179 (ptp) cc_final: 0.8779 (ppp) REVERT: B 2 ILE cc_start: 0.9130 (tp) cc_final: 0.8793 (tp) REVERT: B 10 MET cc_start: 0.5429 (tmm) cc_final: 0.4609 (tmm) REVERT: B 50 GLN cc_start: 0.8303 (tt0) cc_final: 0.7540 (mt0) REVERT: B 66 MET cc_start: 0.7670 (ppp) cc_final: 0.7451 (ppp) REVERT: B 115 ILE cc_start: 0.8975 (mt) cc_final: 0.8769 (mt) REVERT: B 118 MET cc_start: 0.8426 (ptt) cc_final: 0.7748 (tpp) REVERT: B 141 ILE cc_start: 0.8783 (mt) cc_final: 0.8499 (mt) REVERT: B 202 LEU cc_start: 0.8356 (pp) cc_final: 0.8137 (pp) REVERT: C 100 ARG cc_start: 0.7896 (mmp-170) cc_final: 0.7601 (mtm110) REVERT: C 110 THR cc_start: 0.8558 (p) cc_final: 0.7362 (m) REVERT: C 131 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8272 (tttp) REVERT: C 132 ARG cc_start: 0.8309 (ptp-170) cc_final: 0.7566 (ttp-110) REVERT: D 10 MET cc_start: 0.6366 (mmm) cc_final: 0.5190 (ttt) REVERT: D 40 PHE cc_start: 0.8555 (t80) cc_final: 0.8225 (t80) REVERT: D 55 MET cc_start: 0.8990 (ttm) cc_final: 0.8558 (ttm) REVERT: D 96 MET cc_start: 0.3470 (mmp) cc_final: 0.3157 (mmt) REVERT: D 114 GLN cc_start: 0.9277 (pt0) cc_final: 0.8953 (pt0) REVERT: D 118 MET cc_start: 0.8297 (mtt) cc_final: 0.7976 (mmm) REVERT: D 133 TRP cc_start: 0.8503 (m-10) cc_final: 0.8135 (m-10) REVERT: D 199 LYS cc_start: 0.8865 (ptpt) cc_final: 0.8580 (pttt) REVERT: D 213 GLU cc_start: 0.9155 (pt0) cc_final: 0.8929 (pm20) REVERT: E 10 MET cc_start: 0.4337 (mmm) cc_final: 0.3668 (tmm) REVERT: E 63 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8130 (mm-40) REVERT: E 112 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8585 (tp40) REVERT: E 115 ILE cc_start: 0.8823 (mt) cc_final: 0.8532 (mt) REVERT: E 118 MET cc_start: 0.8393 (ptt) cc_final: 0.7631 (tpp) REVERT: E 139 ASN cc_start: 0.8513 (m110) cc_final: 0.8249 (m-40) REVERT: E 202 LEU cc_start: 0.8715 (mm) cc_final: 0.8334 (pp) REVERT: E 212 GLU cc_start: 0.8701 (pm20) cc_final: 0.8379 (pm20) REVERT: E 214 MET cc_start: 0.8901 (mtp) cc_final: 0.8346 (tpt) REVERT: F 25 LYS cc_start: 0.8834 (mttt) cc_final: 0.8267 (tttm) REVERT: F 100 ARG cc_start: 0.8849 (mtp180) cc_final: 0.8398 (mtm110) REVERT: F 131 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8378 (tttp) REVERT: F 140 LYS cc_start: 0.7925 (tppt) cc_final: 0.7551 (tttt) REVERT: F 144 MET cc_start: 0.5792 (tmm) cc_final: 0.5202 (ttm) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.2480 time to fit residues: 135.1698 Evaluate side-chains 319 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 0.0070 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS B 67 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN D 87 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10566 Z= 0.264 Angle : 0.688 9.979 14366 Z= 0.354 Chirality : 0.046 0.164 1604 Planarity : 0.005 0.054 1882 Dihedral : 4.123 20.555 1404 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.18 % Allowed : 0.97 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.20 (0.22), residues: 1310 helix: 0.57 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -0.59 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 117 HIS 0.007 0.001 HIS A 12 PHE 0.018 0.002 PHE D 161 TYR 0.015 0.002 TYR B 169 ARG 0.005 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 389 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6808 (mmm) cc_final: 0.5780 (ttt) REVERT: A 118 MET cc_start: 0.8159 (mtt) cc_final: 0.7845 (mmm) REVERT: A 128 GLU cc_start: 0.7797 (pm20) cc_final: 0.7250 (tm-30) REVERT: A 144 MET cc_start: 0.8416 (ppp) cc_final: 0.8059 (ptt) REVERT: A 161 PHE cc_start: 0.8705 (t80) cc_final: 0.8353 (t80) REVERT: A 203 LYS cc_start: 0.8974 (mttt) cc_final: 0.8689 (mtmm) REVERT: A 213 GLU cc_start: 0.9298 (pt0) cc_final: 0.8878 (pm20) REVERT: A 214 MET cc_start: 0.9216 (ptp) cc_final: 0.8693 (ppp) REVERT: A 215 MET cc_start: 0.8881 (mtm) cc_final: 0.8200 (mtm) REVERT: B 2 ILE cc_start: 0.9089 (tp) cc_final: 0.8848 (tp) REVERT: B 10 MET cc_start: 0.5094 (tmm) cc_final: 0.4323 (tmm) REVERT: B 50 GLN cc_start: 0.8501 (tt0) cc_final: 0.7680 (mt0) REVERT: B 66 MET cc_start: 0.7716 (ppp) cc_final: 0.7433 (ppp) REVERT: B 118 MET cc_start: 0.8463 (ptt) cc_final: 0.7678 (tpp) REVERT: B 141 ILE cc_start: 0.8895 (mt) cc_final: 0.8527 (mt) REVERT: B 144 MET cc_start: 0.8567 (ppp) cc_final: 0.8106 (ppp) REVERT: B 214 MET cc_start: 0.8796 (tpp) cc_final: 0.8127 (tpt) REVERT: C 100 ARG cc_start: 0.8152 (mmp-170) cc_final: 0.7836 (mtm110) REVERT: C 115 ILE cc_start: 0.9599 (mt) cc_final: 0.9393 (tt) REVERT: C 132 ARG cc_start: 0.8422 (ptp-170) cc_final: 0.7736 (ttp-110) REVERT: C 133 TRP cc_start: 0.8148 (m-10) cc_final: 0.7052 (m-10) REVERT: C 144 MET cc_start: 0.6641 (tmm) cc_final: 0.6221 (ttp) REVERT: D 10 MET cc_start: 0.6869 (mmm) cc_final: 0.5815 (ttt) REVERT: D 96 MET cc_start: 0.3571 (mmp) cc_final: 0.3163 (mmt) REVERT: D 114 GLN cc_start: 0.9283 (pt0) cc_final: 0.8941 (pt0) REVERT: D 118 MET cc_start: 0.8366 (mtt) cc_final: 0.8049 (mmm) REVERT: D 131 LYS cc_start: 0.8435 (tttt) cc_final: 0.8160 (tptm) REVERT: D 213 GLU cc_start: 0.9237 (pt0) cc_final: 0.9009 (pm20) REVERT: E 10 MET cc_start: 0.4614 (mmm) cc_final: 0.3853 (tmm) REVERT: E 84 HIS cc_start: 0.7707 (t-170) cc_final: 0.7352 (t-170) REVERT: E 98 GLU cc_start: 0.8693 (tp30) cc_final: 0.8309 (tp30) REVERT: E 115 ILE cc_start: 0.8884 (mt) cc_final: 0.8527 (mt) REVERT: E 118 MET cc_start: 0.8526 (ptt) cc_final: 0.7620 (tpp) REVERT: E 125 PRO cc_start: 0.8272 (Cg_endo) cc_final: 0.8009 (Cg_exo) REVERT: E 139 ASN cc_start: 0.8581 (m110) cc_final: 0.8285 (m110) REVERT: E 202 LEU cc_start: 0.8755 (mm) cc_final: 0.8362 (pp) REVERT: E 214 MET cc_start: 0.8814 (mtp) cc_final: 0.8217 (tpt) REVERT: F 25 LYS cc_start: 0.8756 (mttt) cc_final: 0.8330 (tttm) REVERT: F 131 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8627 (tttm) REVERT: F 132 ARG cc_start: 0.8287 (ptp-170) cc_final: 0.8053 (ptp-170) REVERT: F 140 LYS cc_start: 0.8084 (tppt) cc_final: 0.7567 (tttt) outliers start: 2 outliers final: 0 residues processed: 389 average time/residue: 0.2468 time to fit residues: 129.2054 Evaluate side-chains 304 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0370 chunk 121 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 overall best weight: 2.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10566 Z= 0.212 Angle : 0.687 10.268 14366 Z= 0.351 Chirality : 0.046 0.171 1604 Planarity : 0.005 0.105 1882 Dihedral : 4.146 20.009 1404 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.32 (0.22), residues: 1310 helix: 0.65 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -0.47 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 117 HIS 0.006 0.001 HIS A 12 PHE 0.022 0.002 PHE A 168 TYR 0.020 0.002 TYR F 164 ARG 0.011 0.001 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6678 (mmm) cc_final: 0.5731 (ttt) REVERT: A 118 MET cc_start: 0.8224 (mtt) cc_final: 0.7892 (mmm) REVERT: A 128 GLU cc_start: 0.7736 (pm20) cc_final: 0.7238 (tm-30) REVERT: A 131 LYS cc_start: 0.8615 (tttt) cc_final: 0.8319 (tptm) REVERT: A 161 PHE cc_start: 0.8637 (t80) cc_final: 0.8272 (t80) REVERT: A 203 LYS cc_start: 0.8941 (mttt) cc_final: 0.8656 (mtmm) REVERT: A 213 GLU cc_start: 0.9301 (pt0) cc_final: 0.8885 (pm20) REVERT: A 214 MET cc_start: 0.9218 (ptp) cc_final: 0.8682 (ppp) REVERT: A 215 MET cc_start: 0.8838 (mtm) cc_final: 0.8144 (mtm) REVERT: B 10 MET cc_start: 0.5115 (tmm) cc_final: 0.4391 (tmm) REVERT: B 30 LYS cc_start: 0.7468 (mttt) cc_final: 0.7155 (mttp) REVERT: B 50 GLN cc_start: 0.8443 (tt0) cc_final: 0.7590 (mt0) REVERT: B 58 THR cc_start: 0.8191 (p) cc_final: 0.7959 (t) REVERT: B 66 MET cc_start: 0.7743 (ppp) cc_final: 0.7519 (ppp) REVERT: B 118 MET cc_start: 0.8481 (ptt) cc_final: 0.7997 (ppp) REVERT: B 119 THR cc_start: 0.8982 (m) cc_final: 0.8461 (m) REVERT: B 141 ILE cc_start: 0.8905 (mt) cc_final: 0.8564 (mt) REVERT: B 144 MET cc_start: 0.8367 (ppp) cc_final: 0.7990 (ppp) REVERT: C 100 ARG cc_start: 0.8067 (mmp-170) cc_final: 0.7760 (mtm110) REVERT: C 115 ILE cc_start: 0.9613 (mt) cc_final: 0.9406 (tt) REVERT: C 131 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8209 (tttp) REVERT: C 132 ARG cc_start: 0.8397 (ptp-170) cc_final: 0.7699 (ttp-110) REVERT: C 133 TRP cc_start: 0.7908 (m-10) cc_final: 0.6823 (m-10) REVERT: D 10 MET cc_start: 0.6922 (mmm) cc_final: 0.5938 (ttt) REVERT: D 48 THR cc_start: 0.8943 (p) cc_final: 0.8070 (p) REVERT: D 55 MET cc_start: 0.9025 (ttm) cc_final: 0.8530 (ttm) REVERT: D 96 MET cc_start: 0.3592 (mmp) cc_final: 0.3219 (mmt) REVERT: D 114 GLN cc_start: 0.9272 (pt0) cc_final: 0.8924 (pt0) REVERT: D 118 MET cc_start: 0.8357 (mtt) cc_final: 0.8017 (mmm) REVERT: D 131 LYS cc_start: 0.8413 (tttt) cc_final: 0.8172 (tptm) REVERT: D 213 GLU cc_start: 0.9217 (pt0) cc_final: 0.8980 (pm20) REVERT: E 10 MET cc_start: 0.4308 (mmm) cc_final: 0.3494 (tmm) REVERT: E 84 HIS cc_start: 0.7689 (t-170) cc_final: 0.7300 (t-170) REVERT: E 98 GLU cc_start: 0.8726 (tp30) cc_final: 0.8345 (tp30) REVERT: E 112 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8729 (mm-40) REVERT: E 115 ILE cc_start: 0.8978 (mt) cc_final: 0.8672 (mt) REVERT: E 118 MET cc_start: 0.8544 (ptt) cc_final: 0.7589 (tpp) REVERT: E 125 PRO cc_start: 0.8275 (Cg_endo) cc_final: 0.8009 (Cg_exo) REVERT: E 139 ASN cc_start: 0.8499 (m110) cc_final: 0.8248 (m110) REVERT: E 202 LEU cc_start: 0.8756 (mm) cc_final: 0.8111 (pp) REVERT: E 214 MET cc_start: 0.8878 (mtp) cc_final: 0.8590 (mmm) REVERT: F 25 LYS cc_start: 0.8683 (mttt) cc_final: 0.8297 (tttm) REVERT: F 140 LYS cc_start: 0.8018 (tppt) cc_final: 0.7630 (tttt) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.2483 time to fit residues: 129.4963 Evaluate side-chains 306 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 0.0370 chunk 80 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10566 Z= 0.188 Angle : 0.683 9.258 14366 Z= 0.347 Chirality : 0.046 0.194 1604 Planarity : 0.005 0.050 1882 Dihedral : 4.024 19.610 1404 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1310 helix: 0.71 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.37 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 117 HIS 0.005 0.001 HIS A 12 PHE 0.019 0.002 PHE A 168 TYR 0.018 0.002 TYR F 164 ARG 0.005 0.001 ARG E 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 401 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6674 (mmm) cc_final: 0.5603 (ttt) REVERT: A 40 PHE cc_start: 0.8621 (t80) cc_final: 0.8407 (t80) REVERT: A 118 MET cc_start: 0.8214 (mtt) cc_final: 0.7862 (mmm) REVERT: A 128 GLU cc_start: 0.7689 (pm20) cc_final: 0.7276 (tm-30) REVERT: A 131 LYS cc_start: 0.8542 (tttt) cc_final: 0.8310 (tptm) REVERT: A 161 PHE cc_start: 0.8629 (t80) cc_final: 0.8283 (t80) REVERT: A 203 LYS cc_start: 0.8919 (mttt) cc_final: 0.8620 (mtmm) REVERT: A 213 GLU cc_start: 0.9307 (pt0) cc_final: 0.8881 (pm20) REVERT: A 214 MET cc_start: 0.9196 (ptp) cc_final: 0.8668 (ppp) REVERT: A 215 MET cc_start: 0.8762 (mtm) cc_final: 0.8058 (mtm) REVERT: B 10 MET cc_start: 0.5178 (tmm) cc_final: 0.4438 (tmm) REVERT: B 50 GLN cc_start: 0.8404 (tt0) cc_final: 0.7627 (mt0) REVERT: B 58 THR cc_start: 0.8240 (p) cc_final: 0.7999 (t) REVERT: B 63 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8064 (mm-40) REVERT: B 98 GLU cc_start: 0.7676 (tp30) cc_final: 0.7000 (tp30) REVERT: B 118 MET cc_start: 0.8396 (ptt) cc_final: 0.8005 (ppp) REVERT: B 119 THR cc_start: 0.8898 (m) cc_final: 0.8448 (m) REVERT: B 141 ILE cc_start: 0.8828 (mt) cc_final: 0.8563 (mt) REVERT: B 144 MET cc_start: 0.8390 (ppp) cc_final: 0.7948 (ppp) REVERT: C 100 ARG cc_start: 0.8011 (mmp-170) cc_final: 0.7715 (mtm110) REVERT: C 115 ILE cc_start: 0.9604 (mt) cc_final: 0.9375 (tt) REVERT: C 131 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8279 (tttp) REVERT: C 132 ARG cc_start: 0.8344 (ptp-170) cc_final: 0.7692 (ttp-110) REVERT: C 133 TRP cc_start: 0.7860 (m-10) cc_final: 0.6811 (m-10) REVERT: D 10 MET cc_start: 0.6910 (mmm) cc_final: 0.5970 (ttt) REVERT: D 40 PHE cc_start: 0.8645 (t80) cc_final: 0.8368 (t80) REVERT: D 48 THR cc_start: 0.8936 (p) cc_final: 0.8084 (p) REVERT: D 55 MET cc_start: 0.8957 (ttm) cc_final: 0.8561 (ttm) REVERT: D 96 MET cc_start: 0.3561 (mmp) cc_final: 0.3241 (mmt) REVERT: D 114 GLN cc_start: 0.9254 (pt0) cc_final: 0.8929 (pt0) REVERT: D 118 MET cc_start: 0.8391 (mtt) cc_final: 0.8030 (mmm) REVERT: D 131 LYS cc_start: 0.8399 (tttt) cc_final: 0.8102 (tptm) REVERT: D 133 TRP cc_start: 0.8490 (m-10) cc_final: 0.7910 (m-10) REVERT: D 213 GLU cc_start: 0.9202 (pt0) cc_final: 0.8987 (pm20) REVERT: E 10 MET cc_start: 0.4259 (mmm) cc_final: 0.3436 (tmm) REVERT: E 63 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8079 (mm-40) REVERT: E 76 GLU cc_start: 0.8985 (tt0) cc_final: 0.7882 (tm-30) REVERT: E 84 HIS cc_start: 0.7683 (t-170) cc_final: 0.7249 (t-170) REVERT: E 98 GLU cc_start: 0.8670 (tp30) cc_final: 0.8289 (tp30) REVERT: E 112 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8738 (mm-40) REVERT: E 115 ILE cc_start: 0.8938 (mt) cc_final: 0.8644 (mt) REVERT: E 118 MET cc_start: 0.8508 (ptt) cc_final: 0.7631 (tpp) REVERT: E 125 PRO cc_start: 0.8274 (Cg_endo) cc_final: 0.8025 (Cg_exo) REVERT: E 136 LEU cc_start: 0.8903 (tt) cc_final: 0.8551 (mp) REVERT: E 139 ASN cc_start: 0.8364 (m110) cc_final: 0.8127 (m-40) REVERT: E 202 LEU cc_start: 0.8716 (mm) cc_final: 0.8359 (pp) REVERT: E 210 THR cc_start: 0.7866 (t) cc_final: 0.7478 (t) REVERT: E 214 MET cc_start: 0.8919 (mtp) cc_final: 0.8247 (tpt) REVERT: F 131 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8371 (tttp) REVERT: F 140 LYS cc_start: 0.7841 (tppt) cc_final: 0.7532 (tttt) REVERT: F 149 SER cc_start: 0.9028 (t) cc_final: 0.8655 (p) outliers start: 1 outliers final: 0 residues processed: 401 average time/residue: 0.2507 time to fit residues: 136.9618 Evaluate side-chains 332 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 0.0980 chunk 29 optimal weight: 6.9990 chunk 104 optimal weight: 0.0980 chunk 43 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.131598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.102119 restraints weight = 27765.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105653 restraints weight = 16927.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108020 restraints weight = 11927.392| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10566 Z= 0.183 Angle : 0.687 9.094 14366 Z= 0.347 Chirality : 0.045 0.230 1604 Planarity : 0.005 0.049 1882 Dihedral : 3.920 19.511 1404 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.48 (0.23), residues: 1310 helix: 0.70 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.24 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 117 HIS 0.004 0.001 HIS A 12 PHE 0.022 0.002 PHE B 40 TYR 0.019 0.002 TYR E 164 ARG 0.009 0.001 ARG E 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2893.95 seconds wall clock time: 53 minutes 6.69 seconds (3186.69 seconds total)