Starting phenix.real_space_refine on Tue Feb 13 18:24:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5x_31469/02_2024/7f5x_31469_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5x_31469/02_2024/7f5x_31469.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5x_31469/02_2024/7f5x_31469_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5x_31469/02_2024/7f5x_31469_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5x_31469/02_2024/7f5x_31469_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5x_31469/02_2024/7f5x_31469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5x_31469/02_2024/7f5x_31469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5x_31469/02_2024/7f5x_31469_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5x_31469/02_2024/7f5x_31469_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 52 5.16 5 C 4572 2.51 5 N 1240 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A ASP 266": "OD1" <-> "OD2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 177": "OD1" <-> "OD2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ASP 232": "OD1" <-> "OD2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B ASP 266": "OD1" <-> "OD2" Residue "B ASP 307": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 177": "OD1" <-> "OD2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ASP 232": "OD1" <-> "OD2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "C ASP 266": "OD1" <-> "OD2" Residue "C ASP 307": "OD1" <-> "OD2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "D PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D ASP 266": "OD1" <-> "OD2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 7244 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1801 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 3 Chain: "B" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1801 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 3 Chain: "C" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1801 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 3 Chain: "D" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1801 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Time building chain proxies: 4.32, per 1000 atoms: 0.60 Number of scatterers: 7244 At special positions: 0 Unit cell: (109.18, 87.98, 75.26, 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 52 16.00 O 1380 8.00 N 1240 7.00 C 4572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.3 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 8 sheets defined 44.5% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 50 through 55 removed outlier: 4.119A pdb=" N LYS A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 94 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 118 through 121 No H-bonds generated for 'chain 'A' and resid 118 through 121' Processing helix chain 'A' and resid 143 through 164 removed outlier: 4.734A pdb=" N TYR A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.810A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 322 through 328 removed outlier: 3.508A pdb=" N GLY A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 removed outlier: 4.119A pdb=" N LYS B 54 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 94 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 118 through 121 No H-bonds generated for 'chain 'B' and resid 118 through 121' Processing helix chain 'B' and resid 143 through 164 removed outlier: 4.734A pdb=" N TYR B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 178 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.810A pdb=" N LEU B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 322 through 328 removed outlier: 3.508A pdb=" N GLY B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 55 removed outlier: 4.119A pdb=" N LYS C 54 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 94 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 143 through 164 removed outlier: 4.734A pdb=" N TYR C 164 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 178 Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.810A pdb=" N LEU C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 322 through 328 removed outlier: 3.508A pdb=" N GLY C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 55 removed outlier: 4.119A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 94 Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 118 through 121 No H-bonds generated for 'chain 'D' and resid 118 through 121' Processing helix chain 'D' and resid 143 through 164 removed outlier: 4.734A pdb=" N TYR D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.810A pdb=" N LEU D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 322 through 328 removed outlier: 3.508A pdb=" N GLY D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 168 through 173 removed outlier: 6.637A pdb=" N VAL A 200 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL A 171 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE A 202 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 173 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASN A 204 " --> pdb=" O VAL A 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 248 through 250 removed outlier: 6.672A pdb=" N SER A 311 " --> pdb=" O LEU A 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 168 through 173 removed outlier: 6.637A pdb=" N VAL B 200 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL B 171 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE B 202 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 173 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASN B 204 " --> pdb=" O VAL B 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 248 through 250 removed outlier: 6.672A pdb=" N SER B 311 " --> pdb=" O LEU B 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.637A pdb=" N VAL C 200 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL C 171 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE C 202 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL C 173 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASN C 204 " --> pdb=" O VAL C 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 248 through 250 removed outlier: 6.672A pdb=" N SER C 311 " --> pdb=" O LEU C 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 168 through 173 removed outlier: 6.637A pdb=" N VAL D 200 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL D 171 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE D 202 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL D 173 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASN D 204 " --> pdb=" O VAL D 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 248 through 250 removed outlier: 6.672A pdb=" N SER D 311 " --> pdb=" O LEU D 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 252 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2396 1.34 - 1.46: 1168 1.46 - 1.57: 3676 1.57 - 1.69: 0 1.69 - 1.80: 92 Bond restraints: 7332 Sorted by residual: bond pdb=" C GGL A 801 " pdb=" OXT GGL A 801 " ideal model delta sigma weight residual 1.259 1.231 0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C GGL B 801 " pdb=" OXT GGL B 801 " ideal model delta sigma weight residual 1.259 1.231 0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C GGL D 801 " pdb=" O GGL D 801 " ideal model delta sigma weight residual 1.259 1.231 0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C GGL C 801 " pdb=" O GGL C 801 " ideal model delta sigma weight residual 1.259 1.231 0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C GGL B 801 " pdb=" O GGL B 801 " ideal model delta sigma weight residual 1.259 1.232 0.027 2.00e-02 2.50e+03 1.83e+00 ... (remaining 7327 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.05: 196 107.05 - 113.78: 4264 113.78 - 120.52: 2784 120.52 - 127.25: 2596 127.25 - 133.99: 44 Bond angle restraints: 9884 Sorted by residual: angle pdb=" N ASN B 233 " pdb=" CA ASN B 233 " pdb=" C ASN B 233 " ideal model delta sigma weight residual 110.80 119.46 -8.66 2.13e+00 2.20e-01 1.65e+01 angle pdb=" N ASN D 233 " pdb=" CA ASN D 233 " pdb=" C ASN D 233 " ideal model delta sigma weight residual 110.80 119.46 -8.66 2.13e+00 2.20e-01 1.65e+01 angle pdb=" N ASN C 233 " pdb=" CA ASN C 233 " pdb=" C ASN C 233 " ideal model delta sigma weight residual 110.80 119.46 -8.66 2.13e+00 2.20e-01 1.65e+01 angle pdb=" N ASN A 233 " pdb=" CA ASN A 233 " pdb=" C ASN A 233 " ideal model delta sigma weight residual 110.80 119.46 -8.66 2.13e+00 2.20e-01 1.65e+01 angle pdb=" N THR B 46 " pdb=" CA THR B 46 " pdb=" C THR B 46 " ideal model delta sigma weight residual 114.56 110.16 4.40 1.27e+00 6.20e-01 1.20e+01 ... (remaining 9879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3866 17.98 - 35.96: 468 35.96 - 53.95: 106 53.95 - 71.93: 8 71.93 - 89.91: 28 Dihedral angle restraints: 4476 sinusoidal: 1756 harmonic: 2720 Sorted by residual: dihedral pdb=" CA ASP D 72 " pdb=" C ASP D 72 " pdb=" N ASN D 73 " pdb=" CA ASN D 73 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP B 72 " pdb=" C ASP B 72 " pdb=" N ASN B 73 " pdb=" CA ASN B 73 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP C 72 " pdb=" C ASP C 72 " pdb=" N ASN C 73 " pdb=" CA ASN C 73 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1076 0.073 - 0.146: 96 0.146 - 0.219: 0 0.219 - 0.291: 0 0.291 - 0.364: 4 Chirality restraints: 1176 Sorted by residual: chirality pdb=" CA ASN B 233 " pdb=" N ASN B 233 " pdb=" C ASN B 233 " pdb=" CB ASN B 233 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ASN C 233 " pdb=" N ASN C 233 " pdb=" C ASN C 233 " pdb=" CB ASN C 233 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ASN D 233 " pdb=" N ASN D 233 " pdb=" C ASN D 233 " pdb=" CB ASN D 233 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 1173 not shown) Planarity restraints: 1248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 175 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO B 176 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 176 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 176 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 175 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO D 176 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 176 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 176 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 175 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO A 176 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.021 5.00e-02 4.00e+02 ... (remaining 1245 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 56 2.46 - 3.07: 5044 3.07 - 3.68: 10186 3.68 - 4.29: 14616 4.29 - 4.90: 25106 Nonbonded interactions: 55008 Sorted by model distance: nonbonded pdb=" CE2 TYR B 164 " pdb=" NH2 ARG D 70 " model vdw 1.845 3.420 nonbonded pdb=" NH2 ARG A 70 " pdb=" CE2 TYR C 164 " model vdw 1.845 3.420 nonbonded pdb=" CE2 TYR A 164 " pdb=" NH2 ARG C 70 " model vdw 1.845 3.420 nonbonded pdb=" NH2 ARG B 70 " pdb=" CE2 TYR D 164 " model vdw 1.845 3.420 nonbonded pdb=" CE2 PHE B 108 " pdb=" OE1 GLN D 163 " model vdw 1.896 3.340 ... (remaining 55003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.240 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: 0.000 Extract box with map and model: 5.700 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.310 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.005 0.032 7332 Z= 0.324 Angle : 0.611 8.663 9884 Z= 0.339 Chirality : 0.046 0.364 1176 Planarity : 0.004 0.037 1248 Dihedral : 17.476 89.911 2708 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.46 % Favored : 91.67 % Rotamer: Outliers : 6.15 % Allowed : 26.67 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.25), residues: 912 helix: -1.10 (0.21), residues: 412 sheet: -4.57 (0.32), residues: 164 loop : -2.37 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 304 HIS 0.001 0.001 HIS C 92 PHE 0.008 0.002 PHE D 161 TYR 0.004 0.001 TYR B 164 ARG 0.002 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 216 time to evaluate : 0.867 Fit side-chains REVERT: A 52 GLN cc_start: 0.8001 (mp10) cc_final: 0.7773 (mp10) REVERT: A 123 MET cc_start: 0.3887 (mmt) cc_final: 0.3123 (mtt) REVERT: A 154 MET cc_start: 0.8561 (mmm) cc_final: 0.8299 (mmm) REVERT: A 170 GLN cc_start: 0.8801 (tt0) cc_final: 0.8596 (tt0) REVERT: A 262 PRO cc_start: 0.7700 (Cg_exo) cc_final: 0.7435 (Cg_endo) REVERT: A 272 HIS cc_start: 0.8108 (m-70) cc_final: 0.7856 (m90) REVERT: B 52 GLN cc_start: 0.8003 (mp10) cc_final: 0.7773 (mp10) REVERT: B 123 MET cc_start: 0.3887 (mmt) cc_final: 0.3125 (mtt) REVERT: B 154 MET cc_start: 0.8561 (mmm) cc_final: 0.8298 (mmm) REVERT: B 170 GLN cc_start: 0.8803 (tt0) cc_final: 0.8595 (tt0) REVERT: B 262 PRO cc_start: 0.7701 (Cg_exo) cc_final: 0.7437 (Cg_endo) REVERT: B 272 HIS cc_start: 0.8105 (m-70) cc_final: 0.7855 (m90) REVERT: C 52 GLN cc_start: 0.8002 (mp10) cc_final: 0.7772 (mp10) REVERT: C 123 MET cc_start: 0.3886 (mmt) cc_final: 0.3123 (mtt) REVERT: C 154 MET cc_start: 0.8563 (mmm) cc_final: 0.8297 (mmm) REVERT: C 170 GLN cc_start: 0.8803 (tt0) cc_final: 0.8595 (tt0) REVERT: C 262 PRO cc_start: 0.7701 (Cg_exo) cc_final: 0.7438 (Cg_endo) REVERT: C 272 HIS cc_start: 0.8107 (m-70) cc_final: 0.7857 (m90) REVERT: D 52 GLN cc_start: 0.8002 (mp10) cc_final: 0.7772 (mp10) REVERT: D 123 MET cc_start: 0.3887 (mmt) cc_final: 0.3124 (mtt) REVERT: D 154 MET cc_start: 0.8562 (mmm) cc_final: 0.8301 (mmm) REVERT: D 170 GLN cc_start: 0.8803 (tt0) cc_final: 0.8597 (tt0) REVERT: D 262 PRO cc_start: 0.7700 (Cg_exo) cc_final: 0.7435 (Cg_endo) REVERT: D 272 HIS cc_start: 0.8109 (m-70) cc_final: 0.7856 (m90) outliers start: 48 outliers final: 40 residues processed: 256 average time/residue: 0.1542 time to fit residues: 55.0638 Evaluate side-chains 224 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 184 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 111 GLN A 186 ASN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS B 111 GLN B 186 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 HIS C 111 GLN C 186 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS D 111 GLN D 186 ASN ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7332 Z= 0.255 Angle : 0.522 5.022 9884 Z= 0.280 Chirality : 0.041 0.138 1176 Planarity : 0.005 0.042 1248 Dihedral : 9.220 59.471 1088 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.59 % Allowed : 31.79 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.28), residues: 912 helix: 0.07 (0.24), residues: 416 sheet: -4.04 (0.36), residues: 168 loop : -1.84 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 304 HIS 0.006 0.002 HIS D 74 PHE 0.008 0.002 PHE D 108 TYR 0.009 0.001 TYR A 164 ARG 0.002 0.000 ARG D 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 0.819 Fit side-chains REVERT: A 62 LYS cc_start: 0.8402 (tmtt) cc_final: 0.8122 (tptm) REVERT: A 76 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8364 (tm) REVERT: A 123 MET cc_start: 0.3963 (mmt) cc_final: 0.3171 (mtt) REVERT: A 154 MET cc_start: 0.8536 (mmm) cc_final: 0.8214 (mmm) REVERT: A 170 GLN cc_start: 0.8789 (tt0) cc_final: 0.8552 (tt0) REVERT: A 262 PRO cc_start: 0.7704 (Cg_exo) cc_final: 0.7460 (Cg_endo) REVERT: A 272 HIS cc_start: 0.7936 (m-70) cc_final: 0.7575 (m90) REVERT: B 49 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7531 (mm-30) REVERT: B 52 GLN cc_start: 0.8204 (mp10) cc_final: 0.7998 (mp10) REVERT: B 62 LYS cc_start: 0.8397 (tmtt) cc_final: 0.8121 (tptm) REVERT: B 76 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8363 (tm) REVERT: B 94 GLU cc_start: 0.8288 (tt0) cc_final: 0.7958 (tt0) REVERT: B 123 MET cc_start: 0.3967 (mmt) cc_final: 0.3169 (mtt) REVERT: B 154 MET cc_start: 0.8538 (mmm) cc_final: 0.8213 (mmm) REVERT: B 170 GLN cc_start: 0.8791 (tt0) cc_final: 0.8553 (tt0) REVERT: B 262 PRO cc_start: 0.7707 (Cg_exo) cc_final: 0.7326 (Cg_endo) REVERT: B 272 HIS cc_start: 0.7935 (m-70) cc_final: 0.7575 (m90) REVERT: C 49 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7533 (mm-30) REVERT: C 52 GLN cc_start: 0.8199 (mp10) cc_final: 0.7994 (mp10) REVERT: C 62 LYS cc_start: 0.8400 (tmtt) cc_final: 0.8123 (tptm) REVERT: C 76 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8364 (tm) REVERT: C 94 GLU cc_start: 0.8285 (tt0) cc_final: 0.7958 (tt0) REVERT: C 123 MET cc_start: 0.3961 (mmt) cc_final: 0.3166 (mtt) REVERT: C 154 MET cc_start: 0.8537 (mmm) cc_final: 0.8210 (mmm) REVERT: C 170 GLN cc_start: 0.8789 (tt0) cc_final: 0.8551 (tt0) REVERT: C 262 PRO cc_start: 0.7705 (Cg_exo) cc_final: 0.7325 (Cg_endo) REVERT: C 272 HIS cc_start: 0.7937 (m-70) cc_final: 0.7577 (m90) REVERT: D 49 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7531 (mm-30) REVERT: D 52 GLN cc_start: 0.8199 (mp10) cc_final: 0.7994 (mp10) REVERT: D 62 LYS cc_start: 0.8401 (tmtt) cc_final: 0.8125 (tptm) REVERT: D 76 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8363 (tm) REVERT: D 94 GLU cc_start: 0.8284 (tt0) cc_final: 0.7957 (tt0) REVERT: D 123 MET cc_start: 0.3964 (mmt) cc_final: 0.3168 (mtt) REVERT: D 154 MET cc_start: 0.8536 (mmm) cc_final: 0.8213 (mmm) REVERT: D 170 GLN cc_start: 0.8789 (tt0) cc_final: 0.8551 (tt0) REVERT: D 262 PRO cc_start: 0.7703 (Cg_exo) cc_final: 0.7322 (Cg_endo) REVERT: D 272 HIS cc_start: 0.7937 (m-70) cc_final: 0.7574 (m90) outliers start: 28 outliers final: 20 residues processed: 241 average time/residue: 0.1576 time to fit residues: 52.3816 Evaluate side-chains 223 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 247 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 90 optimal weight: 0.0970 chunk 74 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 204 ASN B 74 HIS B 204 ASN C 74 HIS C 204 ASN D 74 HIS D 204 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7332 Z= 0.247 Angle : 0.515 4.844 9884 Z= 0.279 Chirality : 0.041 0.138 1176 Planarity : 0.004 0.045 1248 Dihedral : 7.247 56.091 1040 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.64 % Allowed : 28.97 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.28), residues: 912 helix: 0.54 (0.25), residues: 416 sheet: -3.91 (0.37), residues: 168 loop : -1.64 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 304 HIS 0.006 0.002 HIS A 74 PHE 0.005 0.002 PHE C 108 TYR 0.004 0.001 TYR D 55 ARG 0.003 0.000 ARG D 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 0.826 Fit side-chains REVERT: A 62 LYS cc_start: 0.8426 (tmtt) cc_final: 0.8175 (tptm) REVERT: A 94 GLU cc_start: 0.8260 (tt0) cc_final: 0.7892 (tt0) REVERT: A 123 MET cc_start: 0.4085 (mmt) cc_final: 0.3298 (mtt) REVERT: A 170 GLN cc_start: 0.8801 (tt0) cc_final: 0.8563 (tt0) REVERT: A 243 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7545 (tm-30) REVERT: A 262 PRO cc_start: 0.7730 (Cg_exo) cc_final: 0.7291 (Cg_endo) REVERT: A 272 HIS cc_start: 0.7951 (m-70) cc_final: 0.7578 (m90) REVERT: B 62 LYS cc_start: 0.8421 (tmtt) cc_final: 0.8169 (tptm) REVERT: B 123 MET cc_start: 0.4088 (mmt) cc_final: 0.3306 (mtt) REVERT: B 170 GLN cc_start: 0.8808 (tt0) cc_final: 0.8566 (tt0) REVERT: B 262 PRO cc_start: 0.7660 (Cg_exo) cc_final: 0.7383 (Cg_endo) REVERT: B 272 HIS cc_start: 0.7945 (m-70) cc_final: 0.7572 (m90) REVERT: C 62 LYS cc_start: 0.8423 (tmtt) cc_final: 0.8169 (tptm) REVERT: C 123 MET cc_start: 0.4084 (mmt) cc_final: 0.3302 (mtt) REVERT: C 170 GLN cc_start: 0.8804 (tt0) cc_final: 0.8563 (tt0) REVERT: C 262 PRO cc_start: 0.7663 (Cg_exo) cc_final: 0.7386 (Cg_endo) REVERT: C 272 HIS cc_start: 0.7946 (m-70) cc_final: 0.7573 (m90) REVERT: D 62 LYS cc_start: 0.8424 (tmtt) cc_final: 0.8172 (tptm) REVERT: D 123 MET cc_start: 0.4085 (mmt) cc_final: 0.3301 (mtt) REVERT: D 170 GLN cc_start: 0.8803 (tt0) cc_final: 0.8563 (tt0) REVERT: D 262 PRO cc_start: 0.7659 (Cg_exo) cc_final: 0.7380 (Cg_endo) REVERT: D 272 HIS cc_start: 0.7947 (m-70) cc_final: 0.7571 (m90) outliers start: 44 outliers final: 32 residues processed: 237 average time/residue: 0.1740 time to fit residues: 55.8198 Evaluate side-chains 235 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 203 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 247 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 74 HIS C 74 HIS D 74 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7332 Z= 0.246 Angle : 0.510 5.001 9884 Z= 0.280 Chirality : 0.040 0.137 1176 Planarity : 0.004 0.047 1248 Dihedral : 7.084 58.355 1040 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.49 % Allowed : 31.54 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.28), residues: 912 helix: 0.75 (0.25), residues: 416 sheet: -3.82 (0.37), residues: 168 loop : -1.64 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 304 HIS 0.007 0.002 HIS C 74 PHE 0.006 0.002 PHE A 178 TYR 0.005 0.001 TYR C 164 ARG 0.003 0.000 ARG D 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 0.819 Fit side-chains REVERT: A 62 LYS cc_start: 0.8440 (tmtt) cc_final: 0.8173 (tptm) REVERT: A 94 GLU cc_start: 0.8225 (tt0) cc_final: 0.7877 (tt0) REVERT: A 123 MET cc_start: 0.4153 (mmt) cc_final: 0.3343 (mtt) REVERT: A 170 GLN cc_start: 0.8823 (tt0) cc_final: 0.8582 (tt0) REVERT: A 243 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 262 PRO cc_start: 0.7729 (Cg_exo) cc_final: 0.7344 (Cg_endo) REVERT: A 272 HIS cc_start: 0.7842 (m-70) cc_final: 0.7500 (m90) REVERT: B 62 LYS cc_start: 0.8433 (tmtt) cc_final: 0.8167 (tptm) REVERT: B 123 MET cc_start: 0.4155 (mmt) cc_final: 0.3348 (mtt) REVERT: B 170 GLN cc_start: 0.8825 (tt0) cc_final: 0.8585 (tt0) REVERT: B 243 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 262 PRO cc_start: 0.7674 (Cg_exo) cc_final: 0.7398 (Cg_endo) REVERT: B 272 HIS cc_start: 0.7842 (m-70) cc_final: 0.7496 (m90) REVERT: C 62 LYS cc_start: 0.8433 (tmtt) cc_final: 0.8168 (tptm) REVERT: C 123 MET cc_start: 0.4151 (mmt) cc_final: 0.3344 (mtt) REVERT: C 170 GLN cc_start: 0.8825 (tt0) cc_final: 0.8586 (tt0) REVERT: C 243 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7571 (tm-30) REVERT: C 262 PRO cc_start: 0.7677 (Cg_exo) cc_final: 0.7403 (Cg_endo) REVERT: C 272 HIS cc_start: 0.7840 (m-70) cc_final: 0.7495 (m90) REVERT: D 62 LYS cc_start: 0.8436 (tmtt) cc_final: 0.8170 (tptm) REVERT: D 123 MET cc_start: 0.4148 (mmt) cc_final: 0.3346 (mtt) REVERT: D 170 GLN cc_start: 0.8825 (tt0) cc_final: 0.8584 (tt0) REVERT: D 243 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7568 (tm-30) REVERT: D 262 PRO cc_start: 0.7672 (Cg_exo) cc_final: 0.7393 (Cg_endo) REVERT: D 272 HIS cc_start: 0.7841 (m-70) cc_final: 0.7495 (m90) outliers start: 35 outliers final: 35 residues processed: 220 average time/residue: 0.1745 time to fit residues: 51.8191 Evaluate side-chains 224 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 189 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 247 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 79 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7332 Z= 0.200 Angle : 0.482 4.990 9884 Z= 0.267 Chirality : 0.039 0.136 1176 Planarity : 0.004 0.047 1248 Dihedral : 6.152 58.769 1028 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.87 % Allowed : 31.92 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.29), residues: 912 helix: 1.00 (0.25), residues: 416 sheet: -3.74 (0.36), residues: 168 loop : -1.50 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 304 HIS 0.006 0.002 HIS A 74 PHE 0.006 0.001 PHE C 108 TYR 0.004 0.001 TYR A 55 ARG 0.002 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 209 time to evaluate : 0.852 Fit side-chains REVERT: A 52 GLN cc_start: 0.7915 (mp10) cc_final: 0.7692 (pt0) REVERT: A 94 GLU cc_start: 0.8202 (tt0) cc_final: 0.7839 (tt0) REVERT: A 123 MET cc_start: 0.4141 (mmt) cc_final: 0.3336 (mtt) REVERT: A 170 GLN cc_start: 0.8800 (tt0) cc_final: 0.8536 (tt0) REVERT: A 243 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7608 (tm-30) REVERT: A 262 PRO cc_start: 0.7642 (Cg_exo) cc_final: 0.7322 (Cg_endo) REVERT: A 272 HIS cc_start: 0.7709 (m-70) cc_final: 0.7339 (m90) REVERT: B 62 LYS cc_start: 0.8391 (tmtt) cc_final: 0.8114 (tptp) REVERT: B 123 MET cc_start: 0.4141 (mmt) cc_final: 0.3342 (mtt) REVERT: B 170 GLN cc_start: 0.8803 (tt0) cc_final: 0.8531 (tt0) REVERT: B 243 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 252 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7140 (mmm) REVERT: B 262 PRO cc_start: 0.7645 (Cg_exo) cc_final: 0.7365 (Cg_endo) REVERT: B 272 HIS cc_start: 0.7772 (m-70) cc_final: 0.7376 (m90) REVERT: C 62 LYS cc_start: 0.8391 (tmtt) cc_final: 0.8111 (tptp) REVERT: C 123 MET cc_start: 0.4137 (mmt) cc_final: 0.3340 (mtt) REVERT: C 170 GLN cc_start: 0.8801 (tt0) cc_final: 0.8529 (tt0) REVERT: C 243 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 252 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7133 (mmm) REVERT: C 262 PRO cc_start: 0.7650 (Cg_exo) cc_final: 0.7369 (Cg_endo) REVERT: C 272 HIS cc_start: 0.7771 (m-70) cc_final: 0.7376 (m90) REVERT: D 62 LYS cc_start: 0.8389 (tmtt) cc_final: 0.8111 (tptp) REVERT: D 123 MET cc_start: 0.4138 (mmt) cc_final: 0.3334 (mtt) REVERT: D 170 GLN cc_start: 0.8802 (tt0) cc_final: 0.8527 (tt0) REVERT: D 243 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7616 (tm-30) REVERT: D 252 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7139 (mmm) REVERT: D 262 PRO cc_start: 0.7646 (Cg_exo) cc_final: 0.7362 (Cg_endo) REVERT: D 272 HIS cc_start: 0.7775 (m-70) cc_final: 0.7380 (m90) outliers start: 38 outliers final: 26 residues processed: 231 average time/residue: 0.1962 time to fit residues: 60.2769 Evaluate side-chains 227 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 252 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7332 Z= 0.236 Angle : 0.506 4.934 9884 Z= 0.277 Chirality : 0.040 0.138 1176 Planarity : 0.004 0.047 1248 Dihedral : 6.135 59.594 1028 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.97 % Allowed : 31.67 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 912 helix: 1.05 (0.25), residues: 420 sheet: -3.68 (0.36), residues: 168 loop : -1.24 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 304 HIS 0.005 0.002 HIS C 74 PHE 0.005 0.001 PHE C 108 TYR 0.004 0.001 TYR C 55 ARG 0.002 0.000 ARG C 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 0.867 Fit side-chains REVERT: A 94 GLU cc_start: 0.8221 (tt0) cc_final: 0.7878 (tt0) REVERT: A 123 MET cc_start: 0.4134 (mmt) cc_final: 0.3347 (mtt) REVERT: A 170 GLN cc_start: 0.8821 (tt0) cc_final: 0.8569 (tt0) REVERT: A 262 PRO cc_start: 0.7616 (Cg_exo) cc_final: 0.7290 (Cg_endo) REVERT: A 272 HIS cc_start: 0.7715 (m-70) cc_final: 0.7289 (m90) REVERT: B 62 LYS cc_start: 0.8323 (tmtt) cc_final: 0.7959 (tptp) REVERT: B 123 MET cc_start: 0.4137 (mmt) cc_final: 0.3354 (mtt) REVERT: B 170 GLN cc_start: 0.8820 (tt0) cc_final: 0.8560 (tt0) REVERT: B 252 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7048 (mmm) REVERT: B 262 PRO cc_start: 0.7648 (Cg_exo) cc_final: 0.7348 (Cg_endo) REVERT: C 62 LYS cc_start: 0.8321 (tmtt) cc_final: 0.7957 (tptp) REVERT: C 123 MET cc_start: 0.4133 (mmt) cc_final: 0.3353 (mtt) REVERT: C 170 GLN cc_start: 0.8819 (tt0) cc_final: 0.8558 (tt0) REVERT: C 252 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7045 (mmm) REVERT: C 262 PRO cc_start: 0.7652 (Cg_exo) cc_final: 0.7351 (Cg_endo) REVERT: D 62 LYS cc_start: 0.8325 (tmtt) cc_final: 0.7959 (tptp) REVERT: D 123 MET cc_start: 0.4130 (mmt) cc_final: 0.3346 (mtt) REVERT: D 170 GLN cc_start: 0.8813 (tt0) cc_final: 0.8553 (tt0) REVERT: D 252 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7051 (mmm) REVERT: D 262 PRO cc_start: 0.7644 (Cg_exo) cc_final: 0.7342 (Cg_endo) outliers start: 31 outliers final: 25 residues processed: 198 average time/residue: 0.1646 time to fit residues: 45.1589 Evaluate side-chains 211 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 252 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7332 Z= 0.214 Angle : 0.503 5.017 9884 Z= 0.277 Chirality : 0.039 0.134 1176 Planarity : 0.004 0.048 1248 Dihedral : 6.000 59.783 1028 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.95 % Allowed : 33.85 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.29), residues: 912 helix: 1.15 (0.25), residues: 420 sheet: -3.60 (0.36), residues: 168 loop : -1.18 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 304 HIS 0.003 0.001 HIS C 74 PHE 0.005 0.001 PHE B 108 TYR 0.003 0.001 TYR A 55 ARG 0.002 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 0.825 Fit side-chains REVERT: A 52 GLN cc_start: 0.7917 (mp10) cc_final: 0.7701 (pt0) REVERT: A 123 MET cc_start: 0.4151 (mmt) cc_final: 0.3355 (mtt) REVERT: A 170 GLN cc_start: 0.8816 (tt0) cc_final: 0.8546 (tt0) REVERT: A 243 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7679 (tm-30) REVERT: A 252 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7108 (mmm) REVERT: A 262 PRO cc_start: 0.7519 (Cg_exo) cc_final: 0.7190 (Cg_endo) REVERT: A 318 MET cc_start: 0.8874 (mpp) cc_final: 0.8663 (mmm) REVERT: B 62 LYS cc_start: 0.8254 (tmtt) cc_final: 0.7876 (tptp) REVERT: B 123 MET cc_start: 0.4152 (mmt) cc_final: 0.3358 (mtt) REVERT: B 170 GLN cc_start: 0.8816 (tt0) cc_final: 0.8559 (tt0) REVERT: B 243 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 262 PRO cc_start: 0.7554 (Cg_exo) cc_final: 0.7251 (Cg_endo) REVERT: C 62 LYS cc_start: 0.8251 (tmtt) cc_final: 0.7874 (tptp) REVERT: C 123 MET cc_start: 0.4150 (mmt) cc_final: 0.3355 (mtt) REVERT: C 170 GLN cc_start: 0.8812 (tt0) cc_final: 0.8556 (tt0) REVERT: C 243 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7684 (tm-30) REVERT: C 262 PRO cc_start: 0.7558 (Cg_exo) cc_final: 0.7255 (Cg_endo) REVERT: D 62 LYS cc_start: 0.8255 (tmtt) cc_final: 0.7877 (tptp) REVERT: D 123 MET cc_start: 0.4149 (mmt) cc_final: 0.3359 (mtt) REVERT: D 170 GLN cc_start: 0.8810 (tt0) cc_final: 0.8555 (tt0) REVERT: D 243 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7685 (tm-30) REVERT: D 262 PRO cc_start: 0.7552 (Cg_exo) cc_final: 0.7247 (Cg_endo) outliers start: 23 outliers final: 18 residues processed: 191 average time/residue: 0.1419 time to fit residues: 38.7442 Evaluate side-chains 193 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 247 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7332 Z= 0.246 Angle : 0.523 5.020 9884 Z= 0.288 Chirality : 0.040 0.135 1176 Planarity : 0.004 0.047 1248 Dihedral : 6.016 59.174 1028 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.85 % Allowed : 32.56 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.29), residues: 912 helix: 1.22 (0.25), residues: 420 sheet: -3.52 (0.37), residues: 168 loop : -1.13 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 304 HIS 0.004 0.001 HIS B 74 PHE 0.005 0.001 PHE A 108 TYR 0.003 0.001 TYR C 55 ARG 0.002 0.000 ARG D 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 0.809 Fit side-chains REVERT: A 123 MET cc_start: 0.4175 (mmt) cc_final: 0.3389 (mtt) REVERT: A 170 GLN cc_start: 0.8826 (tt0) cc_final: 0.8570 (tt0) REVERT: A 186 ASN cc_start: 0.8820 (m-40) cc_final: 0.8396 (m-40) REVERT: A 243 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 252 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7108 (mmm) REVERT: A 262 PRO cc_start: 0.7294 (Cg_exo) cc_final: 0.6951 (Cg_endo) REVERT: A 318 MET cc_start: 0.8909 (mpp) cc_final: 0.8687 (mmm) REVERT: B 123 MET cc_start: 0.4175 (mmt) cc_final: 0.3382 (mtt) REVERT: B 170 GLN cc_start: 0.8828 (tt0) cc_final: 0.8586 (tt0) REVERT: B 186 ASN cc_start: 0.8825 (m-40) cc_final: 0.8411 (m-40) REVERT: B 252 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7049 (mmm) REVERT: B 262 PRO cc_start: 0.7326 (Cg_exo) cc_final: 0.7010 (Cg_endo) REVERT: C 123 MET cc_start: 0.4180 (mmt) cc_final: 0.3392 (mtt) REVERT: C 170 GLN cc_start: 0.8824 (tt0) cc_final: 0.8579 (tt0) REVERT: C 186 ASN cc_start: 0.8819 (m-40) cc_final: 0.8388 (m-40) REVERT: C 252 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7048 (mmm) REVERT: C 262 PRO cc_start: 0.7335 (Cg_exo) cc_final: 0.7013 (Cg_endo) REVERT: D 123 MET cc_start: 0.4173 (mmt) cc_final: 0.3382 (mtt) REVERT: D 170 GLN cc_start: 0.8823 (tt0) cc_final: 0.8579 (tt0) REVERT: D 186 ASN cc_start: 0.8826 (m-40) cc_final: 0.8413 (m-40) REVERT: D 252 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7052 (mmm) REVERT: D 262 PRO cc_start: 0.7325 (Cg_exo) cc_final: 0.7007 (Cg_endo) outliers start: 30 outliers final: 22 residues processed: 205 average time/residue: 0.1484 time to fit residues: 43.6212 Evaluate side-chains 209 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 252 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 0.0070 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7332 Z= 0.199 Angle : 0.526 5.250 9884 Z= 0.292 Chirality : 0.039 0.133 1176 Planarity : 0.004 0.046 1248 Dihedral : 5.768 59.597 1028 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.21 % Allowed : 33.97 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.29), residues: 912 helix: 1.36 (0.24), residues: 420 sheet: -3.30 (0.37), residues: 168 loop : -1.13 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 304 HIS 0.004 0.001 HIS A 74 PHE 0.005 0.001 PHE A 108 TYR 0.003 0.001 TYR B 55 ARG 0.002 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 0.803 Fit side-chains REVERT: A 73 ASN cc_start: 0.7231 (t0) cc_final: 0.6641 (t0) REVERT: A 123 MET cc_start: 0.4156 (mmt) cc_final: 0.3371 (mtt) REVERT: A 186 ASN cc_start: 0.8812 (m-40) cc_final: 0.8379 (m-40) REVERT: A 243 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7602 (tm-30) REVERT: A 260 ASN cc_start: 0.7854 (t0) cc_final: 0.7648 (t0) REVERT: A 262 PRO cc_start: 0.7273 (Cg_exo) cc_final: 0.6898 (Cg_endo) REVERT: A 318 MET cc_start: 0.8917 (mpp) cc_final: 0.8663 (mmm) REVERT: B 62 LYS cc_start: 0.8158 (tmtt) cc_final: 0.7495 (tptm) REVERT: B 73 ASN cc_start: 0.7238 (t0) cc_final: 0.6655 (t0) REVERT: B 123 MET cc_start: 0.4152 (mmt) cc_final: 0.3367 (mtt) REVERT: B 243 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 252 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.6928 (mmm) REVERT: B 262 PRO cc_start: 0.7256 (Cg_exo) cc_final: 0.6931 (Cg_endo) REVERT: C 62 LYS cc_start: 0.8157 (tmtt) cc_final: 0.7492 (tptm) REVERT: C 73 ASN cc_start: 0.7094 (t0) cc_final: 0.6528 (t0) REVERT: C 123 MET cc_start: 0.4161 (mmt) cc_final: 0.3373 (mtt) REVERT: C 186 ASN cc_start: 0.8798 (m-40) cc_final: 0.8358 (m110) REVERT: C 243 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7708 (tm-30) REVERT: C 252 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.6922 (mmm) REVERT: C 262 PRO cc_start: 0.7260 (Cg_exo) cc_final: 0.6938 (Cg_endo) REVERT: D 62 LYS cc_start: 0.8160 (tmtt) cc_final: 0.7499 (tptm) REVERT: D 73 ASN cc_start: 0.7235 (t0) cc_final: 0.6649 (t0) REVERT: D 123 MET cc_start: 0.4149 (mmt) cc_final: 0.3359 (mtt) REVERT: D 243 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7700 (tm-30) REVERT: D 252 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.6931 (mmm) REVERT: D 262 PRO cc_start: 0.7252 (Cg_exo) cc_final: 0.6930 (Cg_endo) outliers start: 25 outliers final: 16 residues processed: 200 average time/residue: 0.1434 time to fit residues: 40.8330 Evaluate side-chains 200 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 252 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7332 Z= 0.218 Angle : 0.532 5.665 9884 Z= 0.296 Chirality : 0.039 0.134 1176 Planarity : 0.004 0.046 1248 Dihedral : 5.528 58.904 1020 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.82 % Allowed : 34.23 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.29), residues: 912 helix: 1.42 (0.24), residues: 424 sheet: -3.20 (0.37), residues: 168 loop : -1.12 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 304 HIS 0.004 0.001 HIS B 74 PHE 0.005 0.001 PHE D 108 TYR 0.003 0.001 TYR A 55 ARG 0.002 0.000 ARG D 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 0.828 Fit side-chains REVERT: A 123 MET cc_start: 0.4153 (mmt) cc_final: 0.3369 (mtt) REVERT: A 186 ASN cc_start: 0.8795 (m-40) cc_final: 0.8365 (m-40) REVERT: A 260 ASN cc_start: 0.7770 (t0) cc_final: 0.7499 (t0) REVERT: A 262 PRO cc_start: 0.7219 (Cg_exo) cc_final: 0.6837 (Cg_endo) REVERT: A 318 MET cc_start: 0.8925 (mpp) cc_final: 0.8681 (mmm) REVERT: B 62 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7461 (tptm) REVERT: B 123 MET cc_start: 0.4153 (mmt) cc_final: 0.3367 (mtt) REVERT: B 243 GLU cc_start: 0.8544 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 252 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.6963 (mmm) REVERT: B 260 ASN cc_start: 0.7749 (t0) cc_final: 0.7522 (t0) REVERT: B 262 PRO cc_start: 0.7224 (Cg_exo) cc_final: 0.6891 (Cg_endo) REVERT: C 62 LYS cc_start: 0.8166 (tmtt) cc_final: 0.7458 (tptm) REVERT: C 123 MET cc_start: 0.4159 (mmt) cc_final: 0.3378 (mtt) REVERT: C 186 ASN cc_start: 0.8787 (m-40) cc_final: 0.8372 (m-40) REVERT: C 243 GLU cc_start: 0.8546 (tm-30) cc_final: 0.7770 (tm-30) REVERT: C 252 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.6931 (mmm) REVERT: C 260 ASN cc_start: 0.7747 (t0) cc_final: 0.7517 (t0) REVERT: C 262 PRO cc_start: 0.7228 (Cg_exo) cc_final: 0.6897 (Cg_endo) REVERT: D 62 LYS cc_start: 0.8161 (tmtt) cc_final: 0.7460 (tptm) REVERT: D 123 MET cc_start: 0.4148 (mmt) cc_final: 0.3360 (mtt) REVERT: D 243 GLU cc_start: 0.8540 (tm-30) cc_final: 0.7763 (tm-30) REVERT: D 252 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.6913 (mmm) REVERT: D 260 ASN cc_start: 0.7753 (t0) cc_final: 0.7525 (t0) REVERT: D 262 PRO cc_start: 0.7219 (Cg_exo) cc_final: 0.6887 (Cg_endo) outliers start: 22 outliers final: 19 residues processed: 181 average time/residue: 0.1500 time to fit residues: 38.9521 Evaluate side-chains 199 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 177 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 320 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.178315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143098 restraints weight = 8660.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148061 restraints weight = 5105.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151289 restraints weight = 3691.374| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7332 Z= 0.238 Angle : 0.542 5.642 9884 Z= 0.301 Chirality : 0.039 0.135 1176 Planarity : 0.004 0.044 1248 Dihedral : 5.474 58.037 1020 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.08 % Allowed : 33.97 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.29), residues: 912 helix: 1.49 (0.24), residues: 424 sheet: -3.14 (0.37), residues: 168 loop : -1.16 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 304 HIS 0.004 0.001 HIS A 74 PHE 0.005 0.001 PHE D 108 TYR 0.003 0.001 TYR A 55 ARG 0.002 0.000 ARG C 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1718.39 seconds wall clock time: 32 minutes 1.33 seconds (1921.33 seconds total)