Starting phenix.real_space_refine on Thu Feb 15 06:12:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8x_35253/02_2024/8i8x_35253_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8x_35253/02_2024/8i8x_35253.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8x_35253/02_2024/8i8x_35253_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8x_35253/02_2024/8i8x_35253_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8x_35253/02_2024/8i8x_35253_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8x_35253/02_2024/8i8x_35253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8x_35253/02_2024/8i8x_35253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8x_35253/02_2024/8i8x_35253_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8x_35253/02_2024/8i8x_35253_updated.pdb" } resolution = 3.25 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= 0.004 sd= 0.018 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 19 5.16 5 C 7069 2.51 5 N 1856 2.21 5 O 2276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 367": "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: 11226 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2709 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 341} Chain: "B" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2709 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 341} Chain: "C" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2709 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 341} Chain: "D" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1695 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 16, 'TRANS': 207} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "F" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 945 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 11, 'TRANS': 179} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 626 Unresolved non-hydrogen angles: 804 Unresolved non-hydrogen dihedrals: 526 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 1, 'TYR:plan': 12, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 361 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 153 Unusual residues: {'KDL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 153 Unusual residues: {'KDL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 153 Unusual residues: {'KDL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.30, per 1000 atoms: 0.56 Number of scatterers: 11226 At special positions: 0 Unit cell: (106.752, 92.574, 144.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 6 15.00 O 2276 8.00 N 1856 7.00 C 7069 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.35 Conformation dependent library (CDL) restraints added in 2.4 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 9 sheets defined 17.0% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 118 through 124 removed outlier: 4.445A pdb=" N SER A 123 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP A 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 225 through 228 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'B' and resid 117 through 124 removed outlier: 3.803A pdb=" N VAL B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TRP B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 225 through 228 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'C' and resid 117 through 124 removed outlier: 4.087A pdb=" N VAL C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 159 No H-bonds generated for 'chain 'C' and resid 156 through 159' Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'D' and resid 21 through 28 Processing helix chain 'D' and resid 30 through 33 No H-bonds generated for 'chain 'D' and resid 30 through 33' Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.604A pdb=" N ALA D 41 " --> pdb=" O PRO D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 73 removed outlier: 3.557A pdb=" N GLU D 62 " --> pdb=" O THR D 58 " (cutoff:3.500A) Proline residue: D 64 - end of helix removed outlier: 3.615A pdb=" N MET D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 92 removed outlier: 3.573A pdb=" N VAL D 81 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 83 " --> pdb=" O GLY D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 116 through 123 removed outlier: 3.590A pdb=" N TYR D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 161 through 180 removed outlier: 3.509A pdb=" N TRP D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 177 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'F' and resid 7 through 24 Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 33 through 42 removed outlier: 3.814A pdb=" N ARG F 37 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR F 38 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN F 42 " --> pdb=" O THR F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 91 Processing helix chain 'F' and resid 162 through 165 No H-bonds generated for 'chain 'F' and resid 162 through 165' Processing helix chain 'F' and resid 169 through 171 No H-bonds generated for 'chain 'F' and resid 169 through 171' Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.388A pdb=" N LYS F 178 " --> pdb=" O THR F 174 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 removed outlier: 4.071A pdb=" N TYR A 25 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 166 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 200 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 217 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 276 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 334 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 362 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 361 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 36 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 60 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 218 through 222 Processing sheet with id= C, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.697A pdb=" N TYR B 25 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B 96 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN B 80 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR B 94 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLN B 82 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER B 92 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 101 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE B 109 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 245 " --> pdb=" O GLY B 215 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 279 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 286 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 316 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B 303 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP B 314 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 335 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 334 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 36 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 64 through 66 Processing sheet with id= E, first strand: chain 'B' and resid 218 through 222 Processing sheet with id= F, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.518A pdb=" N TYR C 25 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS C 27 " --> pdb=" O ASN C 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN C 30 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 60 " --> pdb=" O TYR C 35 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 37 through 45 removed outlier: 3.612A pdb=" N GLY C 40 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 363 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS C 42 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 361 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TYR C 259 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY C 107 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 109 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 101 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 98 " --> pdb=" O GLN C 76 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 76 " --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 246 through 250 Processing sheet with id= I, first strand: chain 'F' and resid 96 through 98 482 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1951 1.30 - 1.43: 3156 1.43 - 1.55: 6194 1.55 - 1.68: 125 1.68 - 1.81: 36 Bond restraints: 11462 Sorted by residual: bond pdb=" CFK KDL B 401 " pdb=" O3 KDL B 401 " ideal model delta sigma weight residual 1.493 1.401 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" CFK KDL A 401 " pdb=" O3 KDL A 401 " ideal model delta sigma weight residual 1.493 1.405 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CFK KDL C 401 " pdb=" O3 KDL C 401 " ideal model delta sigma weight residual 1.493 1.407 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CDO KDL A 401 " pdb=" NAO KDL A 401 " ideal model delta sigma weight residual 1.524 1.446 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" CDO KDL B 401 " pdb=" NAO KDL B 401 " ideal model delta sigma weight residual 1.524 1.446 0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 11457 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.45: 205 107.45 - 114.08: 6126 114.08 - 120.71: 4690 120.71 - 127.35: 4455 127.35 - 133.98: 67 Bond angle restraints: 15543 Sorted by residual: angle pdb=" CAN KDL C 401 " pdb=" NAO KDL C 401 " pdb=" CDO KDL C 401 " ideal model delta sigma weight residual 119.99 131.99 -12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CAN KDL B 401 " pdb=" NAO KDL B 401 " pdb=" CDO KDL B 401 " ideal model delta sigma weight residual 119.99 131.34 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CAN KDL A 401 " pdb=" NAO KDL A 401 " pdb=" CDO KDL A 401 " ideal model delta sigma weight residual 119.99 130.34 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N PHE C 182 " pdb=" CA PHE C 182 " pdb=" C PHE C 182 " ideal model delta sigma weight residual 114.56 110.67 3.89 1.27e+00 6.20e-01 9.38e+00 angle pdb=" CAN KDL C 401 " pdb=" CAP KDL C 401 " pdb=" CAR KDL C 401 " ideal model delta sigma weight residual 112.46 121.39 -8.93 3.00e+00 1.11e-01 8.86e+00 ... (remaining 15538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.05: 6087 29.05 - 58.09: 406 58.09 - 87.14: 51 87.14 - 116.18: 19 116.18 - 145.23: 7 Dihedral angle restraints: 6570 sinusoidal: 2476 harmonic: 4094 Sorted by residual: dihedral pdb=" CGQ KDL A 401 " pdb=" CGN KDL A 401 " pdb=" CGP KDL A 401 " pdb=" OFZ KDL A 401 " ideal model delta sinusoidal sigma weight residual 173.18 -41.59 -145.23 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" CBV KDL B 401 " pdb=" CBX KDL B 401 " pdb=" CBZ KDL B 401 " pdb=" OCA KDL B 401 " ideal model delta sinusoidal sigma weight residual 174.37 -49.63 -136.00 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" CFM KDL C 401 " pdb=" CFK KDL C 401 " pdb=" CFL KDL C 401 " pdb=" O3 KDL C 401 " ideal model delta sinusoidal sigma weight residual 185.98 62.44 123.54 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 6567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1544 0.099 - 0.198: 68 0.198 - 0.297: 9 0.297 - 0.396: 2 0.396 - 0.495: 2 Chirality restraints: 1625 Sorted by residual: chirality pdb=" CAT KDL B 401 " pdb=" CAR KDL B 401 " pdb=" CAV KDL B 401 " pdb=" OAU KDL B 401 " both_signs ideal model delta sigma weight residual False -2.66 -2.17 -0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" CAT KDL C 401 " pdb=" CAR KDL C 401 " pdb=" CAV KDL C 401 " pdb=" OAU KDL C 401 " both_signs ideal model delta sigma weight residual False -2.66 -2.25 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CAT KDL A 401 " pdb=" CAR KDL A 401 " pdb=" CAV KDL A 401 " pdb=" OAU KDL A 401 " both_signs ideal model delta sigma weight residual False -2.66 -2.27 -0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 1622 not shown) Planarity restraints: 2059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CGN KDL A 401 " 0.016 2.00e-02 2.50e+03 9.47e-03 8.96e-01 pdb=" CGP KDL A 401 " -0.005 2.00e-02 2.50e+03 pdb=" OFZ KDL A 401 " -0.005 2.00e-02 2.50e+03 pdb=" OGO KDL A 401 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 KDL C 401 " -0.005 2.00e-02 2.50e+03 7.45e-03 6.94e-01 pdb=" C7 KDL C 401 " 0.013 2.00e-02 2.50e+03 pdb=" C8 KDL C 401 " -0.007 2.00e-02 2.50e+03 pdb=" N2 KDL C 401 " 0.004 2.00e-02 2.50e+03 pdb=" O7 KDL C 401 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 63 " -0.013 5.00e-02 4.00e+02 2.04e-02 6.65e-01 pdb=" N PRO D 64 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " -0.012 5.00e-02 4.00e+02 ... (remaining 2056 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 3573 2.82 - 3.34: 8953 3.34 - 3.86: 18100 3.86 - 4.38: 20069 4.38 - 4.90: 36574 Nonbonded interactions: 87269 Sorted by model distance: nonbonded pdb=" O THR F 66 " pdb=" N ALA F 68 " model vdw 2.294 2.520 nonbonded pdb=" OG SER A 219 " pdb=" OG1 THR A 241 " model vdw 2.331 2.440 nonbonded pdb=" O VAL A 118 " pdb=" OG1 THR A 122 " model vdw 2.340 2.440 nonbonded pdb=" NH1 ARG B 238 " pdb=" OHE KDL B 401 " model vdw 2.345 2.520 nonbonded pdb=" N ASP B 289 " pdb=" OD1 ASP B 289 " model vdw 2.351 2.520 ... (remaining 87264 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' } 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: 1.930 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: 7.230 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 35.260 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.120 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 11462 Z= 0.447 Angle : 0.687 11.996 15543 Z= 0.273 Chirality : 0.049 0.495 1625 Planarity : 0.002 0.020 2059 Dihedral : 20.121 145.226 4020 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.57 % Favored : 97.29 % Rotamer: Outliers : 2.94 % Allowed : 23.28 % Favored : 73.79 % 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: -0.99 (0.22), residues: 1440 helix: -0.17 (0.33), residues: 224 sheet: 0.55 (0.24), residues: 550 loop : -1.93 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 161 HIS 0.001 0.000 HIS B 42 PHE 0.005 0.000 PHE C 290 TYR 0.002 0.000 TYR B 318 ARG 0.001 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 151 THR cc_start: 0.8978 (m) cc_final: 0.8730 (m) REVERT: A 237 ASP cc_start: 0.7633 (p0) cc_final: 0.7214 (t0) REVERT: A 367 PHE cc_start: 0.8300 (p90) cc_final: 0.7995 (p90) REVERT: B 114 ASN cc_start: 0.7971 (t0) cc_final: 0.7729 (t0) REVERT: C 197 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8419 (p0) REVERT: D 48 GLN cc_start: 0.8427 (tp-100) cc_final: 0.8013 (tp-100) REVERT: D 138 SER cc_start: 0.8888 (m) cc_final: 0.8446 (t) outliers start: 29 outliers final: 4 residues processed: 192 average time/residue: 0.2092 time to fit residues: 60.1380 Evaluate side-chains 81 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 359 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 261 GLN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN B 346 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN C 285 GLN C 340 ASN D 26 ASN D 52 ASN D 122 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11462 Z= 0.216 Angle : 0.585 8.514 15543 Z= 0.296 Chirality : 0.044 0.179 1625 Planarity : 0.003 0.027 2059 Dihedral : 17.031 133.833 1922 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.24 % Favored : 95.62 % Rotamer: Outliers : 4.45 % Allowed : 23.79 % Favored : 71.76 % 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: -1.11 (0.22), residues: 1440 helix: 0.13 (0.33), residues: 241 sheet: 0.28 (0.23), residues: 521 loop : -1.93 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 161 HIS 0.004 0.001 HIS B 42 PHE 0.022 0.001 PHE C 103 TYR 0.015 0.001 TYR C 111 ARG 0.005 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 72 time to evaluate : 1.405 Fit side-chains REVERT: A 258 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8284 (pp30) REVERT: C 49 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8366 (t0) REVERT: D 138 SER cc_start: 0.9044 (m) cc_final: 0.8643 (t) outliers start: 44 outliers final: 18 residues processed: 110 average time/residue: 0.1904 time to fit residues: 32.5799 Evaluate side-chains 72 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 182 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 130 optimal weight: 50.0000 chunk 140 optimal weight: 30.0000 chunk 115 optimal weight: 0.0170 chunk 129 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 171 GLN C 287 GLN C 330 ASN D 69 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 11462 Z= 0.534 Angle : 0.752 12.729 15543 Z= 0.383 Chirality : 0.049 0.292 1625 Planarity : 0.004 0.067 2059 Dihedral : 16.955 132.012 1919 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.32 % Favored : 93.54 % Rotamer: Outliers : 5.36 % Allowed : 23.18 % Favored : 71.46 % 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: -1.36 (0.22), residues: 1440 helix: 0.70 (0.36), residues: 236 sheet: -0.20 (0.22), residues: 539 loop : -2.14 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 124 HIS 0.004 0.001 HIS A 42 PHE 0.025 0.002 PHE D 87 TYR 0.019 0.002 TYR C 79 ARG 0.010 0.001 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 50 time to evaluate : 1.269 Fit side-chains REVERT: D 94 MET cc_start: 0.8868 (mtm) cc_final: 0.8631 (mtp) REVERT: D 109 GLN cc_start: 0.8585 (mm110) cc_final: 0.8266 (mm-40) outliers start: 53 outliers final: 32 residues processed: 101 average time/residue: 0.1879 time to fit residues: 31.4580 Evaluate side-chains 80 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 48 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 182 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 50.0000 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 138 optimal weight: 50.0000 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11462 Z= 0.229 Angle : 0.579 10.873 15543 Z= 0.291 Chirality : 0.043 0.198 1625 Planarity : 0.003 0.037 2059 Dihedral : 16.386 127.827 1919 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.79 % Favored : 95.07 % Rotamer: Outliers : 3.85 % Allowed : 24.49 % Favored : 71.66 % 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: -1.22 (0.22), residues: 1440 helix: 1.04 (0.36), residues: 231 sheet: -0.14 (0.22), residues: 533 loop : -2.08 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 161 HIS 0.001 0.000 HIS D 82 PHE 0.012 0.001 PHE C 103 TYR 0.012 0.001 TYR C 79 ARG 0.003 0.000 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 52 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: D 94 MET cc_start: 0.8784 (mtm) cc_final: 0.8540 (mtp) REVERT: D 109 GLN cc_start: 0.8510 (mm110) cc_final: 0.8178 (mm-40) REVERT: D 133 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8717 (mm) REVERT: D 148 MET cc_start: 0.7824 (mmm) cc_final: 0.6919 (mpp) outliers start: 38 outliers final: 28 residues processed: 88 average time/residue: 0.1750 time to fit residues: 25.1840 Evaluate side-chains 75 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 46 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 138 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 9.9990 chunk 78 optimal weight: 0.0040 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11462 Z= 0.150 Angle : 0.523 9.923 15543 Z= 0.262 Chirality : 0.042 0.152 1625 Planarity : 0.002 0.035 2059 Dihedral : 15.678 122.397 1919 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.07 % Favored : 94.79 % Rotamer: Outliers : 3.95 % Allowed : 24.90 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1440 helix: 1.74 (0.38), residues: 211 sheet: -0.02 (0.23), residues: 533 loop : -1.85 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 161 HIS 0.001 0.000 HIS B 42 PHE 0.011 0.001 PHE C 103 TYR 0.009 0.001 TYR B 318 ARG 0.003 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 60 time to evaluate : 1.193 Fit side-chains REVERT: A 57 MET cc_start: 0.8199 (tmm) cc_final: 0.7958 (tmm) REVERT: D 94 MET cc_start: 0.8771 (mtm) cc_final: 0.8525 (mtp) REVERT: D 109 GLN cc_start: 0.8480 (mm110) cc_final: 0.8131 (mm-40) REVERT: D 148 MET cc_start: 0.7841 (mmm) cc_final: 0.7033 (mpp) outliers start: 39 outliers final: 28 residues processed: 97 average time/residue: 0.1722 time to fit residues: 27.3218 Evaluate side-chains 81 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 53 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 182 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11462 Z= 0.242 Angle : 0.558 10.101 15543 Z= 0.280 Chirality : 0.043 0.180 1625 Planarity : 0.003 0.040 2059 Dihedral : 15.440 118.169 1919 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.62 % Favored : 94.24 % Rotamer: Outliers : 5.57 % Allowed : 23.79 % Favored : 70.65 % 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: -0.91 (0.23), residues: 1440 helix: 1.79 (0.38), residues: 213 sheet: -0.19 (0.22), residues: 551 loop : -1.77 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 161 HIS 0.001 0.000 HIS D 82 PHE 0.013 0.001 PHE D 87 TYR 0.011 0.001 TYR C 79 ARG 0.003 0.000 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 53 time to evaluate : 1.299 Fit side-chains REVERT: A 57 MET cc_start: 0.8366 (tmm) cc_final: 0.8071 (tmm) REVERT: A 367 PHE cc_start: 0.8877 (p90) cc_final: 0.8538 (p90) REVERT: D 109 GLN cc_start: 0.8531 (mm110) cc_final: 0.8151 (mm-40) REVERT: D 148 MET cc_start: 0.7919 (mmm) cc_final: 0.7355 (mpp) outliers start: 55 outliers final: 39 residues processed: 103 average time/residue: 0.1784 time to fit residues: 29.2696 Evaluate side-chains 87 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 48 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 180 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 40.0000 chunk 15 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11462 Z= 0.194 Angle : 0.542 9.973 15543 Z= 0.272 Chirality : 0.042 0.159 1625 Planarity : 0.003 0.039 2059 Dihedral : 15.270 116.172 1919 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.83 % Favored : 94.03 % Rotamer: Outliers : 4.55 % Allowed : 24.60 % Favored : 70.85 % 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: -0.89 (0.23), residues: 1440 helix: 1.79 (0.38), residues: 213 sheet: -0.19 (0.22), residues: 551 loop : -1.73 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 161 HIS 0.001 0.000 HIS D 82 PHE 0.010 0.001 PHE C 103 TYR 0.009 0.001 TYR B 318 ARG 0.006 0.000 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 51 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8377 (tmm) cc_final: 0.8050 (tmm) REVERT: D 148 MET cc_start: 0.7933 (mmm) cc_final: 0.7422 (mpp) outliers start: 45 outliers final: 40 residues processed: 94 average time/residue: 0.1706 time to fit residues: 26.3747 Evaluate side-chains 87 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 47 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 182 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 125 optimal weight: 50.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11462 Z= 0.185 Angle : 0.538 9.931 15543 Z= 0.270 Chirality : 0.042 0.156 1625 Planarity : 0.003 0.040 2059 Dihedral : 15.172 115.928 1919 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.56 % Favored : 94.31 % Rotamer: Outliers : 4.25 % Allowed : 25.10 % Favored : 70.65 % 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: -1.03 (0.22), residues: 1440 helix: 1.29 (0.37), residues: 231 sheet: -0.17 (0.22), residues: 551 loop : -1.89 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 161 HIS 0.001 0.000 HIS D 82 PHE 0.010 0.001 PHE C 103 TYR 0.010 0.001 TYR C 79 ARG 0.005 0.000 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 50 time to evaluate : 1.323 Fit side-chains REVERT: A 57 MET cc_start: 0.8392 (tmm) cc_final: 0.8054 (tmm) REVERT: D 70 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8350 (m-10) REVERT: D 148 MET cc_start: 0.7938 (mmm) cc_final: 0.7447 (mpp) outliers start: 42 outliers final: 40 residues processed: 90 average time/residue: 0.1704 time to fit residues: 25.1682 Evaluate side-chains 88 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 47 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 70 TYR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 182 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 50.0000 chunk 120 optimal weight: 0.0670 chunk 128 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11462 Z= 0.151 Angle : 0.532 9.805 15543 Z= 0.265 Chirality : 0.042 0.153 1625 Planarity : 0.003 0.039 2059 Dihedral : 15.057 115.386 1919 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.28 % Favored : 94.58 % Rotamer: Outliers : 3.95 % Allowed : 25.71 % Favored : 70.34 % 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: -1.00 (0.22), residues: 1440 helix: 1.30 (0.37), residues: 231 sheet: -0.13 (0.22), residues: 551 loop : -1.87 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 161 HIS 0.001 0.000 HIS C 42 PHE 0.010 0.001 PHE B 347 TYR 0.009 0.001 TYR B 318 ARG 0.004 0.000 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 51 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 57 MET cc_start: 0.8411 (tmm) cc_final: 0.8063 (tmm) REVERT: D 70 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.8356 (m-10) REVERT: D 109 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8141 (mm-40) REVERT: D 148 MET cc_start: 0.7922 (mmm) cc_final: 0.7425 (mpp) outliers start: 39 outliers final: 34 residues processed: 87 average time/residue: 0.1743 time to fit residues: 24.7842 Evaluate side-chains 83 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 48 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 70 TYR Chi-restraints excluded: chain D residue 138 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 40.0000 chunk 82 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 131 optimal weight: 50.0000 chunk 113 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 11462 Z= 0.523 Angle : 0.707 10.455 15543 Z= 0.358 Chirality : 0.048 0.248 1625 Planarity : 0.004 0.053 2059 Dihedral : 15.527 119.139 1919 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.29 % Favored : 92.57 % Rotamer: Outliers : 4.66 % Allowed : 24.90 % Favored : 70.45 % 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 (0.22), residues: 1440 helix: 0.97 (0.36), residues: 239 sheet: -0.38 (0.22), residues: 563 loop : -2.15 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 161 HIS 0.003 0.001 HIS D 82 PHE 0.022 0.002 PHE D 87 TYR 0.014 0.002 TYR C 136 ARG 0.005 0.001 ARG C 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 47 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: C 331 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8570 (ttm) REVERT: D 70 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.8403 (m-10) REVERT: D 148 MET cc_start: 0.8046 (mmm) cc_final: 0.7600 (mpp) outliers start: 46 outliers final: 38 residues processed: 92 average time/residue: 0.1770 time to fit residues: 26.4932 Evaluate side-chains 84 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 44 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 70 TYR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.102358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073545 restraints weight = 22457.527| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.18 r_work: 0.3162 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11462 Z= 0.204 Angle : 0.570 10.042 15543 Z= 0.285 Chirality : 0.043 0.175 1625 Planarity : 0.003 0.040 2059 Dihedral : 15.243 116.486 1919 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.49 % Favored : 94.38 % Rotamer: Outliers : 3.85 % Allowed : 26.11 % Favored : 70.04 % 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: -1.20 (0.22), residues: 1440 helix: 1.12 (0.37), residues: 235 sheet: -0.28 (0.22), residues: 563 loop : -2.03 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 161 HIS 0.001 0.000 HIS C 42 PHE 0.010 0.001 PHE C 103 TYR 0.010 0.001 TYR C 136 ARG 0.004 0.000 ARG B 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2285.54 seconds wall clock time: 42 minutes 27.41 seconds (2547.41 seconds total)