Starting phenix.real_space_refine on Mon Mar 11 05:07:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/03_2024/8iq4_35657_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/03_2024/8iq4_35657.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/03_2024/8iq4_35657_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/03_2024/8iq4_35657_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/03_2024/8iq4_35657_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/03_2024/8iq4_35657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/03_2024/8iq4_35657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/03_2024/8iq4_35657_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq4_35657/03_2024/8iq4_35657_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.101 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 4555 2.51 5 N 1208 2.21 5 O 1265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 300": "OD1" <-> "OD2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7080 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2065 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1564 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2342 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 238 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 845 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'87Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.97, per 1000 atoms: 0.56 Number of scatterers: 7080 At special positions: 0 Unit cell: (70.2656, 96.6152, 124.063, 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 1265 8.00 N 1208 7.00 C 4555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 10 sheets defined 37.1% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'R' and resid 30 through 59 Processing helix chain 'R' and resid 65 through 93 Processing helix chain 'R' and resid 106 through 138 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 148 through 172 removed outlier: 3.911A pdb=" N VAL R 152 " --> pdb=" O THR R 148 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 196 through 228 Processing helix chain 'R' and resid 244 through 274 Proline residue: R 264 - end of helix Processing helix chain 'R' and resid 283 through 304 removed outlier: 3.826A pdb=" N PHE R 288 " --> pdb=" O GLU R 284 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 312 No H-bonds generated for 'chain 'R' and resid 309 through 312' Processing helix chain 'A' and resid 18 through 38 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 337 through 351 removed outlier: 3.759A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.693A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.876A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.188A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.746A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.039A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.691A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.963A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.693A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.498A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.719A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.289A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 1074 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: 2.35 Time building geometry restraints manager: 2.58 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: 2261 1.34 - 1.46: 1812 1.46 - 1.58: 3078 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 7222 Sorted by residual: bond pdb=" C12 87Q R 401 " pdb=" C22 87Q R 401 " ideal model delta sigma weight residual 1.356 1.540 -0.184 2.00e-02 2.50e+03 8.49e+01 bond pdb=" C24 87Q R 401 " pdb=" C25 87Q R 401 " ideal model delta sigma weight residual 1.381 1.539 -0.158 2.00e-02 2.50e+03 6.24e+01 bond pdb=" C22 87Q R 401 " pdb=" C24 87Q R 401 " ideal model delta sigma weight residual 1.687 1.543 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C10 87Q R 401 " pdb=" C11 87Q R 401 " ideal model delta sigma weight residual 1.407 1.540 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C11 87Q R 401 " pdb=" C12 87Q R 401 " ideal model delta sigma weight residual 1.632 1.553 0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 7217 not shown) Histogram of bond angle deviations from ideal: 100.20 - 110.23: 1452 110.23 - 120.26: 5122 120.26 - 130.29: 3216 130.29 - 140.32: 36 140.32 - 150.35: 1 Bond angle restraints: 9827 Sorted by residual: angle pdb=" C14 87Q R 401 " pdb=" C15 87Q R 401 " pdb=" C16 87Q R 401 " ideal model delta sigma weight residual 152.65 117.48 35.17 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C ARG R 59 " pdb=" N GLN R 60 " pdb=" CA GLN R 60 " ideal model delta sigma weight residual 122.31 115.55 6.76 1.81e+00 3.05e-01 1.40e+01 angle pdb=" CA LEU R 169 " pdb=" CB LEU R 169 " pdb=" CG LEU R 169 " ideal model delta sigma weight residual 116.30 126.09 -9.79 3.50e+00 8.16e-02 7.83e+00 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.75e+00 angle pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " pdb=" CG ASN A 50 " ideal model delta sigma weight residual 112.60 114.92 -2.32 1.00e+00 1.00e+00 5.38e+00 ... (remaining 9822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 3966 26.14 - 52.29: 209 52.29 - 78.43: 20 78.43 - 104.57: 2 104.57 - 130.72: 1 Dihedral angle restraints: 4198 sinusoidal: 1432 harmonic: 2766 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -121.49 35.49 1 1.00e+01 1.00e-02 1.78e+01 dihedral pdb=" C14 87Q R 401 " pdb=" C15 87Q R 401 " pdb=" C16 87Q R 401 " pdb=" C17 87Q R 401 " ideal model delta sinusoidal sigma weight residual 63.98 -165.30 -130.72 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CA ARG R 100 " pdb=" C ARG R 100 " pdb=" N PHE R 101 " pdb=" CA PHE R 101 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 4195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.103: 1169 1.103 - 2.207: 0 2.207 - 3.310: 0 3.310 - 4.414: 0 4.414 - 5.517: 1 Chirality restraints: 1170 Sorted by residual: chirality pdb=" C06 87Q R 401 " pdb=" C05 87Q R 401 " pdb=" C07 87Q R 401 " pdb=" C09 87Q R 401 " both_signs ideal model delta sigma weight residual False 2.77 -2.75 5.52 2.00e-01 2.50e+01 7.61e+02 chirality pdb=" C12 87Q R 401 " pdb=" C11 87Q R 401 " pdb=" C13 87Q R 401 " pdb=" C22 87Q R 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.94 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CA VAL N 37 " pdb=" N VAL N 37 " pdb=" C VAL N 37 " pdb=" CB VAL N 37 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 1167 not shown) Planarity restraints: 1225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 263 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO R 264 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO R 264 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 264 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO B 236 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C THR B 87 " 0.028 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.010 2.00e-02 2.50e+03 ... (remaining 1222 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 954 2.75 - 3.29: 6539 3.29 - 3.83: 12010 3.83 - 4.36: 14169 4.36 - 4.90: 25385 Nonbonded interactions: 59057 Sorted by model distance: nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.218 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.259 2.440 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.263 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.266 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD2 ASP B 163 " model vdw 2.269 2.440 ... (remaining 59052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 3.860 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.830 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 0.184 7222 Z= 0.340 Angle : 0.606 35.171 9827 Z= 0.294 Chirality : 0.166 5.517 1170 Planarity : 0.003 0.047 1225 Dihedral : 15.090 130.718 2395 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.58 % Allowed : 12.77 % Favored : 86.65 % 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: 1.43 (0.27), residues: 930 helix: 3.05 (0.26), residues: 340 sheet: 1.05 (0.35), residues: 206 loop : -1.16 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.001 PHE R 165 TYR 0.012 0.001 TYR A 37 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.842 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 1.1393 time to fit residues: 119.6595 Evaluate side-chains 98 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 365 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7222 Z= 0.348 Angle : 0.749 27.460 9827 Z= 0.352 Chirality : 0.069 1.818 1170 Planarity : 0.004 0.053 1225 Dihedral : 7.098 115.824 1031 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.63 % Allowed : 11.03 % Favored : 85.34 % 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: 1.28 (0.27), residues: 930 helix: 2.83 (0.26), residues: 342 sheet: 0.91 (0.34), residues: 213 loop : -1.16 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.011 0.002 HIS A 357 PHE 0.020 0.002 PHE R 101 TYR 0.018 0.002 TYR B 105 ARG 0.004 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.812 Fit side-chains REVERT: R 61 LYS cc_start: 0.7473 (tppt) cc_final: 0.7256 (mtpt) REVERT: B 219 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7928 (mmt180) REVERT: B 234 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8597 (t80) REVERT: N 95 TYR cc_start: 0.8820 (m-80) cc_final: 0.8534 (m-80) outliers start: 25 outliers final: 12 residues processed: 115 average time/residue: 0.9872 time to fit residues: 120.9793 Evaluate side-chains 112 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.0492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7222 Z= 0.151 Angle : 0.648 25.526 9827 Z= 0.293 Chirality : 0.066 1.820 1170 Planarity : 0.003 0.048 1225 Dihedral : 6.269 91.601 1030 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.03 % Allowed : 12.77 % Favored : 85.20 % 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: 1.48 (0.27), residues: 930 helix: 3.10 (0.26), residues: 344 sheet: 0.99 (0.34), residues: 208 loop : -1.14 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE R 101 TYR 0.012 0.001 TYR A 37 ARG 0.002 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.767 Fit side-chains REVERT: B 234 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8440 (t80) REVERT: N 38 ARG cc_start: 0.8819 (ptt180) cc_final: 0.8485 (ptt180) REVERT: N 95 TYR cc_start: 0.8791 (m-80) cc_final: 0.8549 (m-80) outliers start: 14 outliers final: 8 residues processed: 103 average time/residue: 1.0564 time to fit residues: 115.9112 Evaluate side-chains 104 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 0.0870 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7222 Z= 0.170 Angle : 0.661 25.810 9827 Z= 0.297 Chirality : 0.066 1.797 1170 Planarity : 0.003 0.048 1225 Dihedral : 6.004 74.538 1029 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.32 % Allowed : 13.93 % Favored : 83.74 % 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: 1.58 (0.27), residues: 930 helix: 3.23 (0.26), residues: 342 sheet: 1.00 (0.34), residues: 208 loop : -1.07 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE R 165 TYR 0.013 0.001 TYR A 37 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.837 Fit side-chains REVERT: B 219 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7638 (mtp180) REVERT: B 234 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8468 (t80) REVERT: N 38 ARG cc_start: 0.8824 (ptt180) cc_final: 0.8465 (ptt180) REVERT: N 95 TYR cc_start: 0.8805 (m-80) cc_final: 0.8561 (m-80) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 1.0575 time to fit residues: 120.2372 Evaluate side-chains 107 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 7222 Z= 0.469 Angle : 0.804 27.225 9827 Z= 0.384 Chirality : 0.069 1.753 1170 Planarity : 0.005 0.055 1225 Dihedral : 6.605 64.002 1029 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.06 % Allowed : 13.06 % Favored : 82.87 % 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: 1.12 (0.27), residues: 930 helix: 2.55 (0.26), residues: 343 sheet: 0.94 (0.35), residues: 207 loop : -1.15 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 63 HIS 0.011 0.002 HIS A 357 PHE 0.022 0.003 PHE R 101 TYR 0.021 0.002 TYR A 358 ARG 0.004 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.822 Fit side-chains REVERT: R 57 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7343 (ttt-90) REVERT: A 22 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6888 (ttt180) REVERT: B 172 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: B 219 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7418 (mmp-170) REVERT: B 234 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8693 (t80) REVERT: N 95 TYR cc_start: 0.8833 (m-80) cc_final: 0.8537 (m-80) outliers start: 28 outliers final: 13 residues processed: 109 average time/residue: 0.9907 time to fit residues: 115.3633 Evaluate side-chains 108 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ARG Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7222 Z= 0.156 Angle : 0.657 25.713 9827 Z= 0.299 Chirality : 0.066 1.800 1170 Planarity : 0.003 0.050 1225 Dihedral : 5.984 57.456 1029 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.18 % Allowed : 14.66 % Favored : 83.16 % 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: 1.37 (0.27), residues: 930 helix: 2.98 (0.26), residues: 340 sheet: 0.95 (0.34), residues: 207 loop : -1.13 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE R 165 TYR 0.012 0.001 TYR A 358 ARG 0.002 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.838 Fit side-chains REVERT: B 219 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7249 (mmp-170) REVERT: B 234 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8491 (t80) REVERT: N 38 ARG cc_start: 0.8761 (ptt180) cc_final: 0.8383 (ptt180) REVERT: N 95 TYR cc_start: 0.8785 (m-80) cc_final: 0.8486 (m-80) outliers start: 15 outliers final: 10 residues processed: 107 average time/residue: 1.0916 time to fit residues: 123.9488 Evaluate side-chains 108 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7222 Z= 0.145 Angle : 0.646 25.714 9827 Z= 0.290 Chirality : 0.066 1.791 1170 Planarity : 0.003 0.050 1225 Dihedral : 5.651 58.579 1029 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.18 % Allowed : 15.24 % Favored : 82.58 % 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: 1.52 (0.27), residues: 930 helix: 3.18 (0.26), residues: 340 sheet: 0.96 (0.34), residues: 209 loop : -1.07 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE R 165 TYR 0.013 0.001 TYR A 37 ARG 0.001 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.829 Fit side-chains REVERT: B 234 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8417 (t80) REVERT: N 38 ARG cc_start: 0.8763 (ptt180) cc_final: 0.8391 (ptt180) REVERT: N 95 TYR cc_start: 0.8791 (m-80) cc_final: 0.8568 (m-80) outliers start: 15 outliers final: 9 residues processed: 110 average time/residue: 0.9962 time to fit residues: 116.8873 Evaluate side-chains 108 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.0370 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7222 Z= 0.179 Angle : 0.663 25.926 9827 Z= 0.300 Chirality : 0.066 1.785 1170 Planarity : 0.003 0.050 1225 Dihedral : 5.586 55.977 1029 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.32 % Allowed : 15.09 % Favored : 82.58 % 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 (0.27), residues: 930 helix: 3.14 (0.26), residues: 342 sheet: 0.95 (0.34), residues: 215 loop : -1.06 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE R 165 TYR 0.013 0.001 TYR A 37 ARG 0.001 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.759 Fit side-chains REVERT: B 219 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7277 (mmp-170) REVERT: B 234 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8511 (t80) REVERT: N 38 ARG cc_start: 0.8784 (ptt180) cc_final: 0.8397 (ptt180) REVERT: N 95 TYR cc_start: 0.8811 (m-80) cc_final: 0.8578 (m-80) outliers start: 16 outliers final: 10 residues processed: 108 average time/residue: 1.1236 time to fit residues: 129.2612 Evaluate side-chains 109 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7222 Z= 0.284 Angle : 0.714 26.489 9827 Z= 0.331 Chirality : 0.067 1.767 1170 Planarity : 0.004 0.052 1225 Dihedral : 5.850 56.230 1029 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.47 % Allowed : 15.38 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.27), residues: 930 helix: 2.92 (0.26), residues: 342 sheet: 0.97 (0.34), residues: 212 loop : -1.10 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 63 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE R 165 TYR 0.017 0.002 TYR A 358 ARG 0.003 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.838 Fit side-chains REVERT: B 219 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7268 (mmp-170) REVERT: B 234 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8625 (t80) REVERT: N 38 ARG cc_start: 0.8748 (ptt180) cc_final: 0.8362 (ptt180) REVERT: N 95 TYR cc_start: 0.8825 (m-80) cc_final: 0.8548 (m-80) outliers start: 17 outliers final: 10 residues processed: 112 average time/residue: 1.0636 time to fit residues: 127.0313 Evaluate side-chains 110 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.0060 chunk 41 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.0570 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7222 Z= 0.143 Angle : 0.646 25.554 9827 Z= 0.290 Chirality : 0.066 1.794 1170 Planarity : 0.003 0.050 1225 Dihedral : 5.412 51.773 1029 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.45 % Allowed : 16.11 % Favored : 82.44 % 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: 1.46 (0.27), residues: 930 helix: 3.13 (0.26), residues: 343 sheet: 0.94 (0.34), residues: 209 loop : -1.16 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.020 0.001 PHE R 165 TYR 0.014 0.001 TYR A 37 ARG 0.001 0.000 ARG A 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.802 Fit side-chains REVERT: B 234 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8421 (t80) REVERT: N 38 ARG cc_start: 0.8773 (ptt180) cc_final: 0.8395 (ptt180) REVERT: N 95 TYR cc_start: 0.8796 (m-80) cc_final: 0.8554 (m-80) outliers start: 10 outliers final: 10 residues processed: 107 average time/residue: 1.0631 time to fit residues: 121.0516 Evaluate side-chains 111 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain R residue 260 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113765 restraints weight = 7679.698| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.42 r_work: 0.3201 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7222 Z= 0.175 Angle : 0.662 25.930 9827 Z= 0.300 Chirality : 0.066 1.782 1170 Planarity : 0.003 0.051 1225 Dihedral : 5.363 50.416 1029 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.89 % Allowed : 16.26 % Favored : 81.86 % 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: 1.48 (0.27), residues: 930 helix: 3.13 (0.26), residues: 345 sheet: 0.91 (0.34), residues: 209 loop : -1.13 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.001 PHE R 165 TYR 0.014 0.001 TYR A 37 ARG 0.001 0.000 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2788.02 seconds wall clock time: 50 minutes 18.71 seconds (3018.71 seconds total)